Job ID = 6497531 SRX = SRX495121 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:45:42 prefetch.2.10.7: 1) Downloading 'SRR1198653'... 2020-06-25T21:45:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:48:13 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:48:13 prefetch.2.10.7: 1) 'SRR1198653' was downloaded successfully Read 22970231 spots for SRR1198653/SRR1198653.sra Written 22970231 spots for SRR1198653/SRR1198653.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: 00:00:00 Multiseed full-index search: 00:04:56 22970231 reads; of these: 22970231 (100.00%) were unpaired; of these: 2517580 (10.96%) aligned 0 times 16805637 (73.16%) aligned exactly 1 time 3647014 (15.88%) aligned >1 times 89.04% overall alignment rate Time searching: 00:04:56 Overall time: 00:04:57 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 12 files... [bam_rmdupse_core] 2297006 / 20452651 = 0.1123 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 06:59:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.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 06:59:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:59:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:59:55: 1000000 INFO @ Fri, 26 Jun 2020 07:00:00: 2000000 INFO @ Fri, 26 Jun 2020 07:00:06: 3000000 INFO @ Fri, 26 Jun 2020 07:00:12: 4000000 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 07:00:18: 5000000 INFO @ Fri, 26 Jun 2020 07:00:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.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 07:00:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:00:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:00:23: 6000000 INFO @ Fri, 26 Jun 2020 07:00:25: 1000000 INFO @ Fri, 26 Jun 2020 07:00:29: 7000000 INFO @ Fri, 26 Jun 2020 07:00:30: 2000000 INFO @ Fri, 26 Jun 2020 07:00:35: 8000000 INFO @ Fri, 26 Jun 2020 07:00:35: 3000000 INFO @ Fri, 26 Jun 2020 07:00:41: 4000000 INFO @ Fri, 26 Jun 2020 07:00:41: 9000000 INFO @ Fri, 26 Jun 2020 07:00:46: 5000000 INFO @ Fri, 26 Jun 2020 07:00:47: 10000000 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 07:00:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.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 07:00:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:00:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:00:51: 6000000 INFO @ Fri, 26 Jun 2020 07:00:52: 11000000 INFO @ Fri, 26 Jun 2020 07:00:54: 1000000 INFO @ Fri, 26 Jun 2020 07:00:56: 7000000 INFO @ Fri, 26 Jun 2020 07:00:58: 12000000 INFO @ Fri, 26 Jun 2020 07:01:00: 2000000 INFO @ Fri, 26 Jun 2020 07:01:01: 8000000 INFO @ Fri, 26 Jun 2020 07:01:04: 13000000 INFO @ Fri, 26 Jun 2020 07:01:05: 3000000 INFO @ Fri, 26 Jun 2020 07:01:06: 9000000 INFO @ Fri, 26 Jun 2020 07:01:10: 14000000 INFO @ Fri, 26 Jun 2020 07:01:10: 4000000 INFO @ Fri, 26 Jun 2020 07:01:11: 10000000 INFO @ Fri, 26 Jun 2020 07:01:15: 5000000 INFO @ Fri, 26 Jun 2020 07:01:15: 15000000 INFO @ Fri, 26 Jun 2020 07:01:16: 11000000 INFO @ Fri, 26 Jun 2020 07:01:20: 6000000 INFO @ Fri, 26 Jun 2020 07:01:21: 16000000 INFO @ Fri, 26 Jun 2020 07:01:21: 12000000 INFO @ Fri, 26 Jun 2020 07:01:25: 7000000 INFO @ Fri, 26 Jun 2020 07:01:27: 13000000 INFO @ Fri, 26 Jun 2020 07:01:27: 17000000 INFO @ Fri, 26 Jun 2020 07:01:31: 8000000 INFO @ Fri, 26 Jun 2020 07:01:32: 14000000 INFO @ Fri, 26 Jun 2020 07:01:32: 18000000 INFO @ Fri, 26 Jun 2020 07:01:33: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:01:33: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:01:33: #1 total tags in treatment: 18155645 INFO @ Fri, 26 Jun 2020 07:01:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:01:33: #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 07:01:34: #1 tags after filtering in treatment: 18155645 INFO @ Fri, 26 Jun 2020 07:01:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:01:34: #1 finished! INFO @ Fri, 26 Jun 2020 07:01:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:01:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:01:35: #2 number of paired peaks: 263 WARNING @ Fri, 26 Jun 2020 07:01:35: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Fri, 26 Jun 2020 07:01:35: start model_add_line... INFO @ Fri, 26 Jun 2020 07:01:35: start X-correlation... INFO @ Fri, 26 Jun 2020 07:01:35: end of X-cor INFO @ Fri, 26 Jun 2020 07:01:35: #2 finished! INFO @ Fri, 26 Jun 2020 07:01:35: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 07:01:35: #2 alternative fragment length(s) may be 2,42 bps INFO @ Fri, 26 Jun 2020 07:01:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.05_model.r WARNING @ Fri, 26 Jun 2020 07:01:35: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:01:35: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Fri, 26 Jun 2020 07:01:35: #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 07:01:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:01:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:01:36: 9000000 INFO @ Fri, 26 Jun 2020 07:01:37: 15000000 INFO @ Fri, 26 Jun 2020 07:01:41: 10000000 INFO @ Fri, 26 Jun 2020 07:01:42: 16000000 INFO @ Fri, 26 Jun 2020 07:01:46: 11000000 INFO @ Fri, 26 Jun 2020 07:01:47: 17000000 INFO @ Fri, 26 Jun 2020 07:01:51: 12000000 INFO @ Fri, 26 Jun 2020 07:01:52: 18000000 INFO @ Fri, 26 Jun 2020 07:01:53: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:01:53: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:01:53: #1 total tags in treatment: 18155645 INFO @ Fri, 26 Jun 2020 07:01:53: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:01:53: #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 07:01:53: #1 tags after filtering in treatment: 18155645 INFO @ Fri, 26 Jun 2020 07:01:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:01:53: #1 finished! INFO @ Fri, 26 Jun 2020 07:01:53: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:01:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:01:54: #2 number of paired peaks: 263 WARNING @ Fri, 26 Jun 2020 07:01:54: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Fri, 26 Jun 2020 07:01:54: start model_add_line... INFO @ Fri, 26 Jun 2020 07:01:54: start X-correlation... INFO @ Fri, 26 Jun 2020 07:01:54: end of X-cor INFO @ Fri, 26 Jun 2020 07:01:54: #2 finished! INFO @ Fri, 26 Jun 2020 07:01:54: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 07:01:54: #2 alternative fragment length(s) may be 2,42 bps INFO @ Fri, 26 Jun 2020 07:01:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.10_model.r WARNING @ Fri, 26 Jun 2020 07:01:54: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:01:54: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Fri, 26 Jun 2020 07:01:54: #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 07:01:54: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:01:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:01:56: 13000000 INFO @ Fri, 26 Jun 2020 07:02:01: 14000000 INFO @ Fri, 26 Jun 2020 07:02:04: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:02:06: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:02:11: 16000000 INFO @ Fri, 26 Jun 2020 07:02:16: 17000000 INFO @ Fri, 26 Jun 2020 07:02:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:02:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:02:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.05_summits.bed INFO @ Fri, 26 Jun 2020 07:02:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:02:21: 18000000 INFO @ Fri, 26 Jun 2020 07:02:21: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:02:21: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:02:21: #1 total tags in treatment: 18155645 INFO @ Fri, 26 Jun 2020 07:02:21: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:02:21: #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 07:02:22: #1 tags after filtering in treatment: 18155645 INFO @ Fri, 26 Jun 2020 07:02:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:02:22: #1 finished! INFO @ Fri, 26 Jun 2020 07:02:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:02:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:02:23: #2 number of paired peaks: 263 WARNING @ Fri, 26 Jun 2020 07:02:23: Fewer paired peaks (263) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 263 pairs to build model! INFO @ Fri, 26 Jun 2020 07:02:23: start model_add_line... INFO @ Fri, 26 Jun 2020 07:02:23: start X-correlation... INFO @ Fri, 26 Jun 2020 07:02:23: end of X-cor INFO @ Fri, 26 Jun 2020 07:02:23: #2 finished! INFO @ Fri, 26 Jun 2020 07:02:23: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 07:02:23: #2 alternative fragment length(s) may be 2,42 bps INFO @ Fri, 26 Jun 2020 07:02:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.20_model.r WARNING @ Fri, 26 Jun 2020 07:02:23: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:02:23: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Fri, 26 Jun 2020 07:02:23: #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 07:02:23: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:02:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:02:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:02:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:02:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:02:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.10_summits.bed INFO @ Fri, 26 Jun 2020 07:02:37: Done! pass1 - making usageList (0 chroms): 218 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:02:53: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:03:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:03:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:03:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495121/SRX495121.20_summits.bed INFO @ Fri, 26 Jun 2020 07:03:11: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling