Job ID = 6497574 SRX = SRX747300 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:13:41 prefetch.2.10.7: 1) Downloading 'SRR1634998'... 2020-06-25T22:13:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:16:53 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:16:53 prefetch.2.10.7: 1) 'SRR1634998' was downloaded successfully 2020-06-25T22:17:25 prefetch.2.10.7: 'SRR1634998' has 6 unresolved dependencies 2020-06-25T22:17:25 prefetch.2.10.7: 2) Downloading 'ncbi-acc:BX284601.4?vdb-ctx=refseq'... 2020-06-25T22:17:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:17:51 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:17:51 prefetch.2.10.7: 2) 'ncbi-acc:BX284601.4?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:17:51 prefetch.2.10.7: 3) Downloading 'ncbi-acc:BX284602.4?vdb-ctx=refseq'... 2020-06-25T22:17:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:18:06 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:18:06 prefetch.2.10.7: 3) 'ncbi-acc:BX284602.4?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:18:06 prefetch.2.10.7: 4) Downloading 'ncbi-acc:BX284603.3?vdb-ctx=refseq'... 2020-06-25T22:18:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:19:08 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:19:08 prefetch.2.10.7: 4) 'ncbi-acc:BX284603.3?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:19:08 prefetch.2.10.7: 5) Downloading 'ncbi-acc:BX284604.3?vdb-ctx=refseq'... 2020-06-25T22:19:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:19:24 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:19:24 prefetch.2.10.7: 5) 'ncbi-acc:BX284604.3?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:19:24 prefetch.2.10.7: 6) Downloading 'ncbi-acc:BX284605.4?vdb-ctx=refseq'... 2020-06-25T22:19:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:19:39 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:19:39 prefetch.2.10.7: 6) 'ncbi-acc:BX284605.4?vdb-ctx=refseq' was downloaded successfully 2020-06-25T22:19:39 prefetch.2.10.7: 7) Downloading 'ncbi-acc:BX284606.4?vdb-ctx=refseq'... 2020-06-25T22:19:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:19:56 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:19:56 prefetch.2.10.7: 7) 'ncbi-acc:BX284606.4?vdb-ctx=refseq' was downloaded successfully Read 59934228 spots for SRR1634998/SRR1634998.sra Written 59934228 spots for SRR1634998/SRR1634998.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:07:06 59934228 reads; of these: 59934228 (100.00%) were unpaired; of these: 1480684 (2.47%) aligned 0 times 47329296 (78.97%) aligned exactly 1 time 11124248 (18.56%) aligned >1 times 97.53% overall alignment rate Time searching: 00:07:07 Overall time: 00:07:07 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 48071800 / 58453544 = 0.8224 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 07:36:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 07:36:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:36:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:36:59: 1000000 INFO @ Fri, 26 Jun 2020 07:37:04: 2000000 INFO @ Fri, 26 Jun 2020 07:37:09: 3000000 INFO @ Fri, 26 Jun 2020 07:37:13: 4000000 INFO @ Fri, 26 Jun 2020 07:37:18: 5000000 INFO @ Fri, 26 Jun 2020 07:37:23: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 07:37:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 07:37:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:37:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:37:28: 7000000 INFO @ Fri, 26 Jun 2020 07:37:30: 1000000 INFO @ Fri, 26 Jun 2020 07:37:32: 8000000 INFO @ Fri, 26 Jun 2020 07:37:35: 2000000 INFO @ Fri, 26 Jun 2020 07:37:37: 9000000 INFO @ Fri, 26 Jun 2020 07:37:39: 3000000 INFO @ Fri, 26 Jun 2020 07:37:42: 10000000 INFO @ Fri, 26 Jun 2020 07:37:44: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:37:44: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:37:44: #1 total tags in treatment: 10381744 INFO @ Fri, 26 Jun 2020 07:37:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:37:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:37:44: #1 tags after filtering in treatment: 10381744 INFO @ Fri, 26 Jun 2020 07:37:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:37:44: #1 finished! INFO @ Fri, 26 Jun 2020 07:37:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:37:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:37:44: 4000000 INFO @ Fri, 26 Jun 2020 07:37:45: #2 number of paired peaks: 997 WARNING @ Fri, 26 Jun 2020 07:37:45: Fewer paired peaks (997) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 997 pairs to build model! INFO @ Fri, 26 Jun 2020 07:37:45: start model_add_line... INFO @ Fri, 26 Jun 2020 07:37:45: start X-correlation... INFO @ Fri, 26 Jun 2020 07:37:45: end of X-cor INFO @ Fri, 26 Jun 2020 07:37:45: #2 finished! INFO @ Fri, 26 Jun 2020 07:37:45: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:37:45: #2 alternative fragment length(s) may be 1,29,598 bps INFO @ Fri, 26 Jun 2020 07:37:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.05_model.r WARNING @ Fri, 26 Jun 2020 07:37:45: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:37:45: #2 You may need to consider one of the other alternative d(s): 1,29,598 WARNING @ Fri, 26 Jun 2020 07:37:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:37:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:37:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:37:49: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 07:37:54: 6000000 INFO @ Fri, 26 Jun 2020 07:37:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Fri, 26 Jun 2020 07:37:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:37:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:37:59: 7000000 INFO @ Fri, 26 Jun 2020 07:38:00: 1000000 INFO @ Fri, 26 Jun 2020 07:38:04: 8000000 INFO @ Fri, 26 Jun 2020 07:38:04: 2000000 INFO @ Fri, 26 Jun 2020 07:38:05: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:38:09: 9000000 INFO @ Fri, 26 Jun 2020 07:38:09: 3000000 INFO @ Fri, 26 Jun 2020 07:38:14: 10000000 INFO @ Fri, 26 Jun 2020 07:38:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:38:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:38:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.05_summits.bed INFO @ Fri, 26 Jun 2020 07:38:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:38:14: 4000000 INFO @ Fri, 26 Jun 2020 07:38:16: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:38:16: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:38:16: #1 total tags in treatment: 10381744 INFO @ Fri, 26 Jun 2020 07:38:16: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:38:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:38:16: #1 tags after filtering in treatment: 10381744 INFO @ Fri, 26 Jun 2020 07:38:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:38:16: #1 finished! INFO @ Fri, 26 Jun 2020 07:38:16: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:38:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:38:17: #2 number of paired peaks: 997 WARNING @ Fri, 26 Jun 2020 07:38:17: Fewer paired peaks (997) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 997 pairs to build model! INFO @ Fri, 26 Jun 2020 07:38:17: start model_add_line... INFO @ Fri, 26 Jun 2020 07:38:17: start X-correlation... INFO @ Fri, 26 Jun 2020 07:38:17: end of X-cor INFO @ Fri, 26 Jun 2020 07:38:17: #2 finished! INFO @ Fri, 26 Jun 2020 07:38:17: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:38:17: #2 alternative fragment length(s) may be 1,29,598 bps INFO @ Fri, 26 Jun 2020 07:38:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.10_model.r WARNING @ Fri, 26 Jun 2020 07:38:17: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:38:17: #2 You may need to consider one of the other alternative d(s): 1,29,598 WARNING @ Fri, 26 Jun 2020 07:38:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:38:17: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:38:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:38:19: 5000000 INFO @ Fri, 26 Jun 2020 07:38:24: 6000000 INFO @ Fri, 26 Jun 2020 07:38:29: 7000000 INFO @ Fri, 26 Jun 2020 07:38:33: 8000000 INFO @ Fri, 26 Jun 2020 07:38:36: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:38:38: 9000000 INFO @ Fri, 26 Jun 2020 07:38:43: 10000000 INFO @ Fri, 26 Jun 2020 07:38:45: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:38:45: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:38:45: #1 total tags in treatment: 10381744 INFO @ Fri, 26 Jun 2020 07:38:45: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:38:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:38:45: #1 tags after filtering in treatment: 10381744 INFO @ Fri, 26 Jun 2020 07:38:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:38:45: #1 finished! INFO @ Fri, 26 Jun 2020 07:38:45: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:38:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:38:46: #2 number of paired peaks: 997 WARNING @ Fri, 26 Jun 2020 07:38:46: Fewer paired peaks (997) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 997 pairs to build model! INFO @ Fri, 26 Jun 2020 07:38:46: start model_add_line... INFO @ Fri, 26 Jun 2020 07:38:46: start X-correlation... INFO @ Fri, 26 Jun 2020 07:38:46: end of X-cor INFO @ Fri, 26 Jun 2020 07:38:46: #2 finished! INFO @ Fri, 26 Jun 2020 07:38:46: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:38:46: #2 alternative fragment length(s) may be 1,29,598 bps INFO @ Fri, 26 Jun 2020 07:38:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.20_model.r WARNING @ Fri, 26 Jun 2020 07:38:46: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:38:46: #2 You may need to consider one of the other alternative d(s): 1,29,598 WARNING @ Fri, 26 Jun 2020 07:38:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:38:46: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:38:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:38:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:38:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:38:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.10_summits.bed INFO @ Fri, 26 Jun 2020 07:38:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:39:05: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:39:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:39:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:39:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX747300/SRX747300.20_summits.bed INFO @ Fri, 26 Jun 2020 07:39:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling