Open triciapark opened 1 year ago
Hi, we have a similar problem. I'm running mgatk in tenx mode
mgatk tenx -n 10 -i /Output_CellRanger/AUGU_possorted_genome_bam.bam -n AUGU -o /Output_CellRanger/output_mgatk -b /Output_CellRanger/AUGU_barcodes.txt -bt CB
But as @triciapark we have some missing files.
Here the log
Config file /Output_CellRanger/output_mgatk/.internal/parseltongue/snake.scatter.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 10
Rules claiming more threads will be scaled down.
Job stats:
job count min threads max threads
-------------------------- ------- ------------- -------------
all 1 1 1
call_variants 1 1 1
make_depth_table 1 1 1
make_final_sparse_matrices 1 1 1
process_one_slice 10 1 1
total 14 1 1
Select jobs to execute...
[Tue Jul 4 10:57:08 2023]
rule process_one_slice:
input: /Output_CellRanger/output_mgatk/.internal/samples/barcodes.5.bam.txt
output: /Output_CellRanger/output_mgatk/qc/depth/barcodes.5.depth.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.5.A.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.5.C.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.5.G.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.5.T.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.5.coverage.txt
jobid: 5
reason: Missing output files: /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.5.G.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.5.A.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.5.T.txt, /Output_CellRanger/output_mgatk/qc/depth/barcodes.5.depth.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.5.C.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.5.coverage.txt
wildcards: sample=barcodes.5
resources: tmpdir=/scratch/tmp
[Tue Jul 4 10:57:08 2023]
rule process_one_slice:
input: /Output_CellRanger/output_mgatk/.internal/samples/barcodes.6.bam.txt
output: /Output_CellRanger/output_mgatk/qc/depth/barcodes.6.depth.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.6.A.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.6.C.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.6.G.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.6.T.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.6.coverage.txt
jobid: 10
reason: Missing output files: /Output_CellRanger/output_mgatk/qc/depth/barcodes.6.depth.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.6.G.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.6.coverage.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.6.A.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.6.C.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.6.T.txt
wildcards: sample=barcodes.6
resources: tmpdir=/scratch/tmp
[Tue Jul 4 10:57:08 2023]
rule process_one_slice:
input: /Output_CellRanger/output_mgatk/.internal/samples/barcodes.3.bam.txt
output: /Output_CellRanger/output_mgatk/qc/depth/barcodes.3.depth.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.3.A.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.3.C.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.3.G.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.3.T.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.3.coverage.txt
jobid: 7
reason: Missing output files: /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.3.A.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.3.coverage.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.3.C.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.3.T.txt, /Output_CellRanger/output_mgatk/qc/depth/barcodes.3.depth.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.3.G.txt
wildcards: sample=barcodes.3
resources: tmpdir=/scratch/tmp
[Tue Jul 4 10:57:08 2023]
rule process_one_slice:
input: /Output_CellRanger/output_mgatk/.internal/samples/barcodes.1.bam.txt
output: /Output_CellRanger/output_mgatk/qc/depth/barcodes.1.depth.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.1.A.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.1.C.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.1.G.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.1.T.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.1.coverage.txt
jobid: 4
reason: Missing output files: /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.1.T.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.1.C.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.1.A.txt, /Output_CellRanger/output_mgatk/qc/depth/barcodes.1.depth.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.1.coverage.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.1.G.txt
wildcards: sample=barcodes.1
resources: tmpdir=/scratch/tmp
[Tue Jul 4 10:57:08 2023]
rule process_one_slice:
input: /Output_CellRanger/output_mgatk/.internal/samples/barcodes.4.bam.txt
output: /Output_CellRanger/output_mgatk/qc/depth/barcodes.4.depth.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.4.A.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.4.C.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.4.G.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.4.T.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.4.coverage.txt
jobid: 3
reason: Missing output files: /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.4.T.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.4.G.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.4.C.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.4.A.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.4.coverage.txt, /Output_CellRanger/output_mgatk/qc/depth/barcodes.4.depth.txt
wildcards: sample=barcodes.4
resources: tmpdir=/scratch/tmp
[Tue Jul 4 10:57:08 2023]
rule process_one_slice:
input: /Output_CellRanger/output_mgatk/.internal/samples/barcodes.2.bam.txt
output: /Output_CellRanger/output_mgatk/qc/depth/barcodes.2.depth.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.2.A.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.2.C.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.2.G.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.2.T.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.2.coverage.txt
jobid: 9
reason: Missing output files: /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.2.T.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.2.C.txt, /Output_CellRanger/output_mgatk/qc/depth/barcodes.2.depth.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.2.A.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.2.coverage.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.2.G.txt
wildcards: sample=barcodes.2
resources: tmpdir=/scratch/tmp
[Tue Jul 4 10:57:08 2023]
rule process_one_slice:
input: /Output_CellRanger/output_mgatk/.internal/samples/barcodes.9.bam.txt
output: /Output_CellRanger/output_mgatk/qc/depth/barcodes.9.depth.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.9.A.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.9.C.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.9.G.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.9.T.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.9.coverage.txt
jobid: 6
reason: Missing output files: /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.9.A.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.9.C.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.9.G.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.9.T.txt, /Output_CellRanger/output_mgatk/qc/depth/barcodes.9.depth.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.9.coverage.txt
wildcards: sample=barcodes.9
resources: tmpdir=/scratch/tmp
[Tue Jul 4 10:57:08 2023]
rule process_one_slice:
input: /Output_CellRanger/output_mgatk/.internal/samples/barcodes.8.bam.txt
output: /Output_CellRanger/output_mgatk/qc/depth/barcodes.8.depth.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.8.A.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.8.C.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.8.G.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.8.T.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.8.coverage.txt
jobid: 2
reason: Missing output files: /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.8.coverage.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.8.A.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.8.T.txt, /Output_CellRanger/output_mgatk/qc/depth/barcodes.8.depth.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.8.G.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.8.C.txt
wildcards: sample=barcodes.8
resources: tmpdir=/scratch/tmp
[Tue Jul 4 10:57:08 2023]
rule process_one_slice:
input: /Output_CellRanger/output_mgatk/.internal/samples/barcodes.10.bam.txt
output: /Output_CellRanger/output_mgatk/qc/depth/barcodes.10.depth.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.10.A.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.10.C.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.10.G.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.10.T.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.10.coverage.txt
jobid: 11
reason: Missing output files: /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.10.A.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.10.T.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.10.coverage.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.10.C.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.10.G.txt, /Output_CellRanger/output_mgatk/qc/depth/barcodes.10.depth.txt
wildcards: sample=barcodes.10
resources: tmpdir=/scratch/tmp
[Tue Jul 4 10:57:08 2023]
rule process_one_slice:
input: /Output_CellRanger/output_mgatk/.internal/samples/barcodes.7.bam.txt
output: /Output_CellRanger/output_mgatk/qc/depth/barcodes.7.depth.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.7.A.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.7.C.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.7.G.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.7.T.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.7.coverage.txt
jobid: 8
reason: Missing output files:
/Output_CellRanger/output_mgatk/qc/depth/barcodes.7.depth.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.7.G.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.7.T.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.7.C.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.7.A.txt, /Output_CellRanger/output_mgatk/temp/sparse_matrices/barcodes.7.coverage.txt
wildcards: sample=barcodes.7
resources: tmpdir=/scratch/tmp
Config file /Output_CellRanger/output_mgatk/.internal/parseltongue/snake.scatter.yaml is extended by additional config specified via the command line.
Config file /Output_CellRanger/output_mgatk/.internal/parseltongue/snake.scatter.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Config file /Output_CellRanger/output_mgatk/.internal/parseltongue/snake.scatter.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Config file /Output_CellRanger/output_mgatk/.internal/parseltongue/snake.scatter.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Building DAG of jobs...
Config file /Output_CellRanger/output_mgatk/.internal/parseltongue/snake.scatter.yaml is extended by additional config specified via the command line.
Using shell: /usr/bin/bash
Provided cores: 10
Rules claiming more threads will be scaled down.
Select jobs to execute...
Using shell: /usr/bin/bash
Provided cores: 10
Rules claiming more threads will be scaled down.
Select jobs to execute...
Using shell: /usr/bin/bash
Provided cores: 10
Rules claiming more threads will be scaled down.
Select jobs to execute...
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 10
Rules claiming more threads will be scaled down.
Select jobs to execute...
Config file /Output_CellRanger/output_mgatk/.internal/parseltongue/snake.scatter.yaml is extended by additional config specified via the command line.
Using shell: /usr/bin/bash
Provided cores: 10
Rules claiming more threads will be scaled down.
Select jobs to execute...
Config file /Output_CellRanger/output_mgatk/.internal/parseltongue/snake.scatter.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Config file /Output_CellRanger/output_mgatk/.internal/parseltongue/snake.scatter.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 10
Rules claiming more threads will be scaled down.
Select jobs to execute...
Config file /Output_CellRanger/output_mgatk/.internal/parseltongue/snake.scatter.yaml is extended by additional config specified via the command line.
Using shell: /usr/bin/bash
Provided cores: 10
Rules claiming more threads will be scaled down.
Select jobs to execute...
Config file /Output_CellRanger/output_mgatk/.internal/parseltongue/snake.scatter.yaml is extended by additional config specified via the command line.
Using shell: /usr/bin/bash
Provided cores: 10
Rules claiming more threads will be scaled down.
Select jobs to execute...
Building DAG of jobs...
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 10
Rules claiming more threads will be scaled down.
Select jobs to execute...
Using shell: /usr/bin/bash
Provided cores: 10
Rules claiming more threads will be scaled down.
Select jobs to execute...
Error in checkGrep(grep(".A.txt", files)) :
Improper folder specification; file missing / extra file present. See documentation
Calls: importMito -> checkGrep
Execution halted
This is the listo of the output files:
.:
total 30K
drwxr-sr-x 2 cvt 3 Jul 3 09:45 final
drwxr-sr-x 4 cvt 7 Jul 3 09:46 logs
drwxr-sr-x 4 cvt 4 Jul 3 09:46 qc
./final:
total 114K
-rw-r--r-- 1 cvt 119K Jul 4 10:55 chrM_refAllele.txt
./logs:
total 9.0K
-rw-r--r-- 1 cvt 778 Jul 4 10:57 AUGU.parameters.txt
-rw-r--r-- 1 cvt 0 Jul 4 10:57 AUGU.snakemake_tenx.log
-rw-r--r-- 1 cvt 4.9K Jul 4 10:57 base.mgatk.log
drwxr-sr-x 2 cvt 2 Jul 3 09:46 filterlogs
drwxr-sr-x 2 cvt 2 Jul 3 09:46 rmdupslogs
./logs/filterlogs:
total 0
./logs/rmdupslogs:
total 0
./qc:
total 1.0K
drwxr-sr-x 2 cvt 2 Jul 3 09:46 depth
drwxr-sr-x 2 cvt 2 Jul 3 09:46 quality
./qc/depth:
total 0
./qc/quality:
total 0
I also tried with the test file
mgatk bcall -i test_barcode.bam -n bc1 -o bc1dmem -bt CB -b test_barcodes.txt -z`
but I have the same error
`[W::hts_idx_load3] The index file is older than the data file: bc1dmem/temp/barcoded_bams/GCCTAGGCAGTTCGGC-1.bam.bai
[W::hts_idx_load3] The index file is older than the data file: bc1dmem/temp/barcoded_bams/CTAACTTAGAGCCACA-1.bam.bai
[W::hts_idx_load3] The index file is older than the data file: bc1dmem/temp/barcoded_bams/CACCACTAGGAGGCGA-1.bam.bai
Config file bc1dmem/.internal/parseltongue/snake.gather.yaml is extended by additional config specified via the command line.
Config file bc1dmem/.internal/parseltongue/snake.scatter.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Building DAG of jobs...
Using shell: /usr/bin/bash
Using shell: /usr/bin/bash
Provided cores: 10
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Rules claiming more threads will be scaled down.
Job stats:
job count min threads max threads
------------------ ------- ------------- -------------
all 1 1 1
make_sample_list 1 1 1
process_one_sample 6 1 1
total 8 1 1
Job stats:
job count min threads max threads
-------------------------- ------- ------------- -------------
all 1 1 1
make_depth_table 1 1 1
make_final_sparse_matrices 1 1 1
total 3 1 1
Select jobs to execute...
Select jobs to execute...
[Tue Jul 4 13:20:36 2023]
rule make_depth_table:
output: bc1dmem/final/bc1.depthTable.txt
jobid: 1
reason: Missing output files: bc1dmem/final/bc1.depthTable.txt
resources: tmpdir=/scratch/tmp
[Tue Jul 4 13:20:36 2023]
rule process_one_sample:
input: bc1dmem/.internal/samples/CTAACTTAGAGCCACA-1.bam.txt
output: bc1dmem/temp/ready_bam/CTAACTTAGAGCCACA-1.qc.bam, bc1dmem/temp/ready_bam/CTAACTTAGAGCCACA-1.qc.bam.bai, bc1dmem/qc/depth/CTAACTTAGAGCCACA-1.depth.txt, bc1dmem/temp/sparse_matrices/CTAACTTAGAGCCACA-1.A.txt, bc1dmem/temp/sparse_matrices/CTAACTTAGAGCCACA-1.C.txt, bc1dmem/temp/sparse_matrices/CTAACTTAGAGCCACA-1.G.txt, bc1dmem/temp/sparse_matrices/CTAACTTAGAGCCACA-1.T.txt, bc1dmem/temp/sparse_matrices/CTAACTTAGAGCCACA-1.coverage.txt
jobid: 6
reason: Missing output files: bc1dmem/qc/depth/CTAACTTAGAGCCACA-1.depth.txt
wildcards: sample=CTAACTTAGAGCCACA-1
resources: tmpdir=/scratch/tmp
[Tue Jul 4 13:20:36 2023]
rule process_one_sample:
input: bc1dmem/.internal/samples/barcodes.3.bam.txt
output: bc1dmem/temp/ready_bam/barcodes.3.qc.bam, bc1dmem/temp/ready_bam/barcodes.3.qc.bam.bai, bc1dmem/qc/depth/barcodes.3.depth.txt, bc1dmem/temp/sparse_matrices/barcodes.3.A.txt, bc1dmem/temp/sparse_matrices/barcodes.3.C.txt, bc1dmem/temp/sparse_matrices/barcodes.3.G.txt, bc1dmem/temp/sparse_matrices/barcodes.3.T.txt, bc1dmem/temp/sparse_matrices/barcodes.3.coverage.txt
jobid: 4
reason: Missing output files: bc1dmem/qc/depth/barcodes.3.depth.txt
wildcards: sample=barcodes.3
resources: tmpdir=/scratch/tmp
[Tue Jul 4 13:20:36 2023]
rule process_one_sample:
input: bc1dmem/.internal/samples/CACCACTAGGAGGCGA-1.bam.txt
output: bc1dmem/temp/ready_bam/CACCACTAGGAGGCGA-1.qc.bam, bc1dmem/temp/ready_bam/CACCACTAGGAGGCGA-1.qc.bam.bai, bc1dmem/qc/depth/CACCACTAGGAGGCGA-1.depth.txt, bc1dmem/temp/sparse_matrices/CACCACTAGGAGGCGA-1.A.txt, bc1dmem/temp/sparse_matrices/CACCACTAGGAGGCGA-1.C.txt, bc1dmem/temp/sparse_matrices/CACCACTAGGAGGCGA-1.G.txt, bc1dmem/temp/sparse_matrices/CACCACTAGGAGGCGA-1.T.txt, bc1dmem/temp/sparse_matrices/CACCACTAGGAGGCGA-1.coverage.txt
jobid: 5
reason: Missing output files: bc1dmem/qc/depth/CACCACTAGGAGGCGA-1.depth.txt
wildcards: sample=CACCACTAGGAGGCGA-1
resources: tmpdir=/scratch/tmp
[Tue Jul 4 13:20:36 2023]
rule process_one_sample:
input: bc1dmem/.internal/samples/barcodes.2.bam.txt
output: bc1dmem/temp/ready_bam/barcodes.2.qc.bam, bc1dmem/temp/ready_bam/barcodes.2.qc.bam.bai, bc1dmem/qc/depth/barcodes.2.depth.txt, bc1dmem/temp/sparse_matrices/barcodes.2.A.txt, bc1dmem/temp/sparse_matrices/barcodes.2.C.txt, bc1dmem/temp/sparse_matrices/barcodes.2.G.txt, bc1dmem/temp/sparse_matrices/barcodes.2.T.txt, bc1dmem/temp/sparse_matrices/barcodes.2.coverage.txt
jobid: 7
reason: Missing output files: bc1dmem/qc/depth/barcodes.2.depth.txt
wildcards: sample=barcodes.2
resources: tmpdir=/scratch/tmp
[Tue Jul 4 13:20:36 2023]
rule process_one_sample:
input: bc1dmem/.internal/samples/barcodes.1.bam.txt
output: bc1dmem/temp/ready_bam/barcodes.1.qc.bam, bc1dmem/temp/ready_bam/barcodes.1.qc.bam.bai, bc1dmem/qc/depth/barcodes.1.depth.txt, bc1dmem/temp/sparse_matrices/barcodes.1.A.txt, bc1dmem/temp/sparse_matrices/barcodes.1.C.txt, bc1dmem/temp/sparse_matrices/barcodes.1.G.txt, bc1dmem/temp/sparse_matrices/barcodes.1.T.txt, bc1dmem/temp/sparse_matrices/barcodes.1.coverage.txt
jobid: 2
reason: Missing output files: bc1dmem/qc/depth/barcodes.1.depth.txt
wildcards: sample=barcodes.1
resources: tmpdir=/scratch/tmp
[Tue Jul 4 13:20:36 2023]
rule process_one_sample:
input: bc1dmem/.internal/samples/GCCTAGGCAGTTCGGC-1.bam.txt
output: bc1dmem/temp/ready_bam/GCCTAGGCAGTTCGGC-1.qc.bam, bc1dmem/temp/ready_bam/GCCTAGGCAGTTCGGC-1.qc.bam.bai, bc1dmem/qc/depth/GCCTAGGCAGTTCGGC-1.depth.txt, bc1dmem/temp/sparse_matrices/GCCTAGGCAGTTCGGC-1.A.txt, bc1dmem/temp/sparse_matrices/GCCTAGGCAGTTCGGC-1.C.txt, bc1dmem/temp/sparse_matrices/GCCTAGGCAGTTCGGC-1.G.txt, bc1dmem/temp/sparse_matrices/GCCTAGGCAGTTCGGC-1.T.txt, bc1dmem/temp/sparse_matrices/GCCTAGGCAGTTCGGC-1.coverage.txt
jobid: 3
reason: Missing output files: bc1dmem/qc/depth/GCCTAGGCAGTTCGGC-1.depth.txt
wildcards: sample=GCCTAGGCAGTTCGGC-1
resources: tmpdir=/scratch/tmp
Config file bc1dmem/.internal/parseltongue/snake.gather.yaml is extended by additional config specified via the command line.
Config file bc1dmem/.internal/parseltongue/snake.scatter.yaml is extended by additional config specified via the command line.
Config file bc1dmem/.internal/parseltongue/snake.scatter.yaml is extended by additional config specified via the command line.
Config file bc1dmem/.internal/parseltongue/snake.scatter.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Building DAG of jobs...
Building DAG of jobs...
Building DAG of jobs...
Config file bc1dmem/.internal/parseltongue/snake.scatter.yaml is extended by additional config specified via the command line.
Config file bc1dmem/.internal/parseltongue/snake.scatter.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Config file bc1dmem/.internal/parseltongue/snake.scatter.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Select jobs to execute...
Using shell: /usr/bin/bash
Provided cores: 10
Rules claiming more threads will be scaled down.
Select jobs to execute...
Using shell: /usr/bin/bash
Provided cores: 10
Rules claiming more threads will be scaled down.
Select jobs to execute...
Using shell: /usr/bin/bash
Provided cores: 10
Rules claiming more threads will be scaled down.
Select jobs to execute...
Using shell: /usr/bin/bash
Provided cores: 10
Rules claiming more threads will be scaled down.
Select jobs to execute...
Using shell: /usr/bin/bash
Provided cores: 10
Rules claiming more threads will be scaled down.
Using shell: /usr/bin/bash
Select jobs to execute...
Provided cores: 10
Rules claiming more threads will be scaled down.
Select jobs to execute...
[Tue Jul 4 13:20:39 2023]
Finished job 1.
1 of 3 steps (33%) done
Select jobs to execute...
[Tue Jul 4 13:20:39 2023]
rule make_final_sparse_matrices:
output: bc1dmem/final/bc1.A.txt.gz, bc1dmem/final/bc1.C.txt.gz, bc1dmem/final/bc1.G.txt.gz, bc1dmem/final/bc1.T.txt.gz, bc1dmem/final/bc1.coverage.txt.gz
jobid: 2
reason: Missing output files: bc1dmem/final/bc1.G.txt.gz, bc1dmem/final/bc1.A.txt.gz, bc1dmem/final/bc1.C.txt.gz, bc1dmem/final/bc1.T.txt.gz, bc1dmem/final/bc1.coverage.txt.gz
resources: tmpdir=/scratch/tmp
[W::hts_idx_load3] The index file is older than the data file: bc1dmem/temp/barcoded_bams/GCCTAGGCAGTTCGGC-1.bam.bai
[W::hts_idx_load3] The index file is older than the data file: bc1dmem/temp/barcoded_bams/CACCACTAGGAGGCGA-1.bam.bai
[W::hts_idx_load3] The index file is older than the data file: bc1dmem/temp/barcoded_bams/CTAACTTAGAGCCACA-1.bam.bai
Config file bc1dmem/.internal/parseltongue/snake.gather.yaml is extended by additional config specified via the command line.
Building DAG of jobs...
Using shell: /usr/bin/bash
Provided cores: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Select jobs to execute...
gzip: bc1dmem/final/bc1.A.txt: No such file or directory
gzip: bc1dmem/final/bc1.C.txt: No such file or directory
gzip: bc1dmem/final/bc1.G.txt: No such file or directory
gzip: bc1dmem/final/bc1.T.txt: No such file or directory
gzip: bc1dmem/final/bc1.coverage.txt: No such file or directory
Waiting at most 5 seconds for missing files.
Error in checkGrep(grep(".A.txt", files)) :
Improper folder specification; file missing / extra file present. See documentation
Calls: importMito -> checkGrep
Execution halted
I am using the following versions: Python 3.11.4 R 4.2.0 Snakemake 7.30.1
Hi all, apologies for the delayed response-- these seem like two separate issues.
@triciapark it looks like you are erroring out in the remove duplicates
step-- do you have java
in your environment?
@teresa1997 your issue looks to be where the final R script is not running that collates the data. My guess is that you are missing R packages (GenomicRanges, data.table, SummarizedExperiment, Matrix
)
Hi @caleblareau thanks for the answer. The packages are installed. Any other guess?
Hi @caleblareau I also met this problem. All required R package are installed. My java version is
openjdk version "1.8.0_332"
OpenJDK Runtime Environment (Zulu 8.62.0.19-CA-linux64) (build 1.8.0_332-b09)
OpenJDK 64-Bit Server VM (Zulu 8.62.0.19-CA-linux64) (build 25.332-b09, mixed mode)
Hello, I've been following the wiki to try to run mgatk tenx (v0.6.1) on 10x scRNA data using the following command:
But it seems like there are some missing files. This is the log file:
And ls -lRh of the output folder shows this:
Additional Information: I was able to run mgatk on the example code with the call
mgatk tenx -i test_barcode.bam -b test_barcodes.txt -o mgatk_results/test -n test -bt CB -c 2
I am using the following versions: Python 3.9.7 R 4.0.0 Snakemake 7.8.5