hiv-tutorial fails with haplotype_reconstruction: savage, and SAVAGE command output is dumped into terminal instead of log

[Masterxilo]

here's the log... savage failed on all three samples... the output was not put into a log file:

Activating conda environment: .snakemake/conda/e6edb6f18a80cf5f3d8af13ded28a55d_
patch 3 - De novo overlap computations - RunningProcessing output[Fri Nov 18 13:13:47 2022]
Finished job 30.
26 of 30 steps (87%) done
patch 9 - De novo overlap computations - Running rust-overlapsINFO      2022-11-18 13:13:51       SamToFastq

********** NOTE: Picard's command line syntax is changing.
**********
********** For more information, please see:
********** https://github.com/broadinstitute/picard/wiki/Command-Line-Syntax-Transition-For-Users-(Pre-Transition)
**********
********** The command line looks like this in the new syntax:
**********
**********    SamToFastq -I samples/CAP217/4390/alignments/REF_aln.bam -FASTQ samples/CAP217/4390/variants/global/R1.fastq -SECOND_END_FASTQ samples/CAP217/4390/variants/global/R2.fastq -RC false
**********


patch 10 - De novo overlap computations - Running rust-overlaps13:13:51.522 INFO  NativeLibraryLoader - Loading libgkl_compression.so from jar:file:/home/ubuntu/new-vpipe-haplotype-recon-experiments/work-hiv-example/.snakemake/conda/e6edb6f18a80cf5f3d8af13ded28a55d_/share/picard-2.22.3-0/picard.jar!/com/intel/gkl/native/libgkl_compression.so
[Fri Nov 18 13:13:51 CET 2022] SamToFastq INPUT=samples/CAP217/4390/alignments/REF_aln.bam FASTQ=samples/CAP217/4390/variants/global/R1.fastq SECOND_END_FASTQ=samples/CAP217/4390/variants/global/R2.fastq RE_REVERSE=false    OUTPUT_PER_RG=false COMPRESS_OUTPUTS_PER_RG=false RG_TAG=PU INTERLEAVE=false INCLUDE_NON_PF_READS=false CLIPPING_MIN_LENGTH=0 READ1_TRIM=0 READ2_TRIM=0 INCLUDE_NON_PRIMARY_ALIGNMENTS=false VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
[Fri Nov 18 13:13:51 CET 2022] Executing as ubuntu@TIM-N716 on Linux 5.10.102.1-microsoft-standard-WSL2 amd64; OpenJDK 64-Bit Server VM 11.0.8-internal+0-adhoc..src; Deflater: Intel; Inflater: Intel; Provider GCS is not available; Picard version: 2.22.3
WARNING: BAM index file /home/ubuntu/new-vpipe-haplotype-recon-experiments/work-hiv-example/samples/CAP217/4390/alignments/REF_aln.bam.bai is older than BAM /home/ubuntu/new-vpipe-haplotype-recon-experiments/work-hiv-example/samples/CAP217/4390/alignments/REF_aln.bam
patch 3 - De novo overlap computations - RunningProcessing output[Fri Nov 18 13:13:51 CET 2022] picard.sam.SamToFastq done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=536870912
patch 11 - De novo overlap computations - Running rust-overlaps
-------------------------------------------
SAVAGE - Strain Aware VirAl GEnome assembly
-------------------------------------------
Version: 0.4.2
Author: Jasmijn Baaijens
    
Command used:
/home/ubuntu/new-vpipe-haplotype-recon-experiments/work-hiv-example/.snakemake/conda/e6edb6f18a80cf5f3d8af13ded28a55d_/opt/savage-0.4.2/savage.py -t 1 --split 20 -p1 /home/ubuntu/new-vpipe-haplotype-recon-experiments/work-hiv-example/samples/CAP217/4390/variants/global/R1.fastq -p2 /home/ubuntu/new-vpipe-haplotype-recon-experiments/work-hiv-example/samples/CAP217/4390/variants/global/R2.fastq -o samples/CAP217/4390/variants/global/

Parameter values:
filtering = True
reference = None
merge_contigs = 0.0
remove_branches = True
contig_len_stage_c = 100
split_num = 20
use_subreads = True
no_assembly = False
diploid_contig_len = 200
overlap_stage_c = 100
input_p2 = /home/ubuntu/new-vpipe-haplotype-recon-experiments/work-hiv-example/samples/CAP217/4390/variants/global/R2.fastq
input_p1 = /home/ubuntu/new-vpipe-haplotype-recon-experiments/work-hiv-example/samples/CAP217/4390/variants/global/R1.fastq
count_strains = False
min_clique_size = 4
diploid_overlap_len = 30
compute_overlaps = True
preprocessing = True
threads = 1
stage_a = True
stage_b = True
stage_c = True
max_tip_len = None
min_overlap_len = None
outdir = samples/CAP217/4390/variants/global/
average_read_len = None
sfo_mm = 50
revcomp = False
input_s = None
diploid = False

Input fastq stats:
Number of single-end reads = 0
Number of paired-end reads = 4872
Total number of bases = 1398543
Average sequence length = 287.1

Using max_tip_len = 287
Using min_overlap_len = 172

*******************
Preprocessing input
Done!                                                        s 
********************
Overlap computations
Done!                                                            t nningProcessing output 
**************
SAVAGE Stage a
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [33, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [10, 0]
Processing outputpipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [8, 0]
patch 7 - De novo overlap computationspipeline_per_stage.py  
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [3, 0]
 - Running rust-overlapspipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [0, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [0, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [0, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [1, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [33, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [9, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [0, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [1, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [16, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [4, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [1, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [15, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [0, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [2, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [33, 0]
pipeline_per_stage.py
Processing outputStage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [1, 0]
combine_contigs.py
cat: stage_a/patch0/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch1/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch2/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch3/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch4/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch5/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch6/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch7/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch9/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch10/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch11/stage_a/singles.fastq: No such file or directory
Processing outputcat: stage_a/patch12/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch13/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch14/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch15/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch16/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch17/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch18/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch19/stage_a/singles.fastq: No such file or directory
patch 8 - De novo overlap computationsDone!                  
**************
SAVAGE Stage b
Empty set of contigs from Stage a (contigs_stage_a.fasta) --> Exiting SAVAGE.
[Fri Nov 18 13:13:58 2022]
Error in rule savage:
    jobid: 41
    input: samples/CAP188/30/alignments/REF_aln.bam
    output: samples/CAP188/30/variants/global/R1.fastq, samples/CAP188/30/variants/global/R2.fastq, samples/CAP188/30/variants/global/contigs_stage_c.fasta
    log: samples/CAP188/30/variants/global/savage.out.log, samples/CAP188/30/variants/global/savage.err.log (check log file(s) for error message)
    conda-env: /home/ubuntu/new-vpipe-haplotype-recon-experiments/work-hiv-example/.snakemake/conda/e6edb6f18a80cf5f3d8af13ded28a55d_
    shell:
        
            # Convert BAM to FASTQ without re-reversing reads - SAVAGE expect all reads in the same direction
            source /home/ubuntu/new-vpipe-haplotype-recon-experiments/V-pipe/workflow/scripts/functions.sh
            SamToFastq picard I=samples/CAP188/30/alignments/REF_aln.bam FASTQ=samples/CAP188/30/variants/global/R1.fastq SECOND_END_FASTQ=samples/CAP188/30/variants/global/R2.fastq RC=false 2> >(tee samples/CAP188/30/variants/global/savage.err.log >&2)
            # Remove /1 and /2 from the read names
            sed -i -e "s:/1$::" samples/CAP188/30/variants/global/R1.fastq
            sed -i -e "s:/2$::" samples/CAP188/30/variants/global/R2.fastq

            R1=${PWD}/samples/CAP188/30/variants/global/R1.fastq
            R2=${PWD}/samples/CAP188/30/variants/global/R2.fastq
            savage -t 1 --split 20 -p1 ${R1} -p2 ${R2} -o samples/CAP188/30/variants/global/ 2> >(tee -a samples/CAP188/30/variants/global/savage.err.log >&2)
            
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job savage since they might be corrupted:
samples/CAP188/30/variants/global/R1.fastq, samples/CAP188/30/variants/global/R2.fastq
Done!                                                            t 
**************
SAVAGE Stage a
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [127, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [11, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [16, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [63, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [15, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [18, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [36, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [70, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [48, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [98, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [12, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [14, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [111, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [58, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [51, 0]
Processing outputpipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [53, 0]
pipeline_per_stage.py
patch 8 - De novo overlap computationsStage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [68, 0]
 - Running rust-overlapspipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [9, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [32, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [52, 0]
combine_contigs.py
cat: stage_a/patch0/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch1/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch2/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch3/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch4/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch5/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch6/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch7/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch8/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch9/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch10/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch11/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch12/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch13/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch14/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch15/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch17/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch19/stage_a/singles.fastq: No such file or directory
Done!
**************
SAVAGE Stage b
Empty set of contigs from Stage a (contigs_stage_a.fasta) --> Exiting SAVAGE.
[Fri Nov 18 13:14:09 2022]
Error in rule savage:
    jobid: 39
    input: samples/CAP188/4/alignments/REF_aln.bam
    output: samples/CAP188/4/variants/global/R1.fastq, samples/CAP188/4/variants/global/R2.fastq, samples/CAP188/4/variants/global/contigs_stage_c.fasta
    log: samples/CAP188/4/variants/global/savage.out.log, samples/CAP188/4/variants/global/savage.err.log (check log file(s) for error message)
    conda-env: /home/ubuntu/new-vpipe-haplotype-recon-experiments/work-hiv-example/.snakemake/conda/e6edb6f18a80cf5f3d8af13ded28a55d_
    shell:
        
            # Convert BAM to FASTQ without re-reversing reads - SAVAGE expect all reads in the same direction
            source /home/ubuntu/new-vpipe-haplotype-recon-experiments/V-pipe/workflow/scripts/functions.sh
            SamToFastq picard I=samples/CAP188/4/alignments/REF_aln.bam FASTQ=samples/CAP188/4/variants/global/R1.fastq SECOND_END_FASTQ=samples/CAP188/4/variants/global/R2.fastq RC=false 2> >(tee samples/CAP188/4/variants/global/savage.err.log >&2)
            # Remove /1 and /2 from the read names
            sed -i -e "s:/1$::" samples/CAP188/4/variants/global/R1.fastq
            sed -i -e "s:/2$::" samples/CAP188/4/variants/global/R2.fastq

            R1=${PWD}/samples/CAP188/4/variants/global/R1.fastq
            R2=${PWD}/samples/CAP188/4/variants/global/R2.fastq
            savage -t 1 --split 20 -p1 ${R1} -p2 ${R2} -o samples/CAP188/4/variants/global/ 2> >(tee -a samples/CAP188/4/variants/global/savage.err.log >&2)
            
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job savage since they might be corrupted:
samples/CAP188/4/variants/global/R1.fastq, samples/CAP188/4/variants/global/R2.fastq
Done!                                                            t 
**************
SAVAGE Stage a
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [31, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [13, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [56, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [18, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [29, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [25, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [34, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [51, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [193, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [55, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [29, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [25, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [83, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [18, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [85, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [9, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [3, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [28, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [44, 0]
pipeline_per_stage.py
Stage a done in 1 iterations
Maximum read length per iteration:      [0]
Number of contigs per iteration:        [0]
Number of overlaps per iteration:       [27, 0]
combine_contigs.py
cat: stage_a/patch0/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch1/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch2/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch3/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch4/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch5/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch6/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch7/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch9/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch10/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch11/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch13/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch14/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch15/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch16/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch17/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch18/stage_a/singles.fastq: No such file or directory
cat: stage_a/patch19/stage_a/singles.fastq: No such file or directory
Done!
**************
SAVAGE Stage b
Empty set of contigs from Stage a (contigs_stage_a.fasta) --> Exiting SAVAGE.
[Fri Nov 18 13:14:31 2022]
Error in rule savage:
    jobid: 40
    input: samples/CAP217/4390/alignments/REF_aln.bam
    output: samples/CAP217/4390/variants/global/R1.fastq, samples/CAP217/4390/variants/global/R2.fastq, samples/CAP217/4390/variants/global/contigs_stage_c.fasta
    log: samples/CAP217/4390/variants/global/savage.out.log, samples/CAP217/4390/variants/global/savage.err.log (check log file(s) for error message)
    conda-env: /home/ubuntu/new-vpipe-haplotype-recon-experiments/work-hiv-example/.snakemake/conda/e6edb6f18a80cf5f3d8af13ded28a55d_
    shell:
        
            # Convert BAM to FASTQ without re-reversing reads - SAVAGE expect all reads in the same direction
            source /home/ubuntu/new-vpipe-haplotype-recon-experiments/V-pipe/workflow/scripts/functions.sh
            SamToFastq picard I=samples/CAP217/4390/alignments/REF_aln.bam FASTQ=samples/CAP217/4390/variants/global/R1.fastq SECOND_END_FASTQ=samples/CAP217/4390/variants/global/R2.fastq RC=false 2> >(tee samples/CAP217/4390/variants/global/savage.err.log >&2)
            # Remove /1 and /2 from the read names
            sed -i -e "s:/1$::" samples/CAP217/4390/variants/global/R1.fastq
            sed -i -e "s:/2$::" samples/CAP217/4390/variants/global/R2.fastq

            R1=${PWD}/samples/CAP217/4390/variants/global/R1.fastq
            R2=${PWD}/samples/CAP217/4390/variants/global/R2.fastq
            savage -t 1 --split 20 -p1 ${R1} -p2 ${R2} -o samples/CAP217/4390/variants/global/ 2> >(tee -a samples/CAP217/4390/variants/global/savage.err.log >&2)
            
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Removing output files of failed job savage since they might be corrupted:
samples/CAP217/4390/variants/global/R1.fastq, samples/CAP217/4390/variants/global/R2.fastq
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2022-11-18T125029.533222.snakemake.log

I followed https://github.com/cbg-ethz/V-pipe/blob/master/docs/tutorial_hiv.md, my config was

general:
    virus_base_config: 'hiv'
    # e.g: 'hiv', 'sars-cov-2', or absent

    
    # enable hyplotype reconstruction

    # let's try
    haplotype_reconstruction: savage

    # this failed:
    #haplotype_reconstruction: predicthaplo

    # this worked:
    #haplotype_reconstruction: haploclique

input:
    samples_file: samples.tsv

output:
    datadir: samples/

    trim_primers: false
    # see: config/README.md#amplicon-protocols
    snv: false
    local: false

    # enable hyplotype reconstruction
    global: true
    
    
    visualization: false
    diversity: false
    QA: false
    upload: false
    dehumanized_raw_reads: false