Job ID = 6507965 SRX = SRX495123 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:16:49 prefetch.2.10.7: 1) Downloading 'SRR1198655'... 2020-06-26T13:16:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:19:07 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:19:07 prefetch.2.10.7: 1) 'SRR1198655' was downloaded successfully Read 22970231 spots for SRR1198655/SRR1198655.sra Written 22970231 spots for SRR1198655/SRR1198655.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: 00:04:58 22970231 reads; of these: 22970231 (100.00%) were unpaired; of these: 2517088 (10.96%) aligned 0 times 16806175 (73.17%) aligned exactly 1 time 3646968 (15.88%) aligned >1 times 89.04% overall alignment rate Time searching: 00:04:58 Overall time: 00:04:58 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] 2297388 / 20453143 = 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 22:30:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.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 22:30:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:30:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:30:41: 1000000 INFO @ Fri, 26 Jun 2020 22:30:46: 2000000 INFO @ Fri, 26 Jun 2020 22:30:51: 3000000 INFO @ Fri, 26 Jun 2020 22:30:56: 4000000 INFO @ Fri, 26 Jun 2020 22:31:01: 5000000 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 22:31:06: 6000000 INFO @ Fri, 26 Jun 2020 22:31:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.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 22:31:06: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:31:06: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:31:11: 7000000 INFO @ Fri, 26 Jun 2020 22:31:12: 1000000 INFO @ Fri, 26 Jun 2020 22:31:16: 8000000 INFO @ Fri, 26 Jun 2020 22:31:17: 2000000 INFO @ Fri, 26 Jun 2020 22:31:21: 9000000 INFO @ Fri, 26 Jun 2020 22:31:23: 3000000 INFO @ Fri, 26 Jun 2020 22:31:26: 10000000 INFO @ Fri, 26 Jun 2020 22:31:29: 4000000 INFO @ Fri, 26 Jun 2020 22:31:31: 11000000 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 22:31:34: 5000000 INFO @ Fri, 26 Jun 2020 22:31:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.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 22:31:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:31:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:31:36: 12000000 INFO @ Fri, 26 Jun 2020 22:31:40: 6000000 INFO @ Fri, 26 Jun 2020 22:31:41: 13000000 INFO @ Fri, 26 Jun 2020 22:31:41: 1000000 INFO @ Fri, 26 Jun 2020 22:31:46: 7000000 INFO @ Fri, 26 Jun 2020 22:31:46: 14000000 INFO @ Fri, 26 Jun 2020 22:31:47: 2000000 INFO @ Fri, 26 Jun 2020 22:31:51: 15000000 INFO @ Fri, 26 Jun 2020 22:31:51: 8000000 INFO @ Fri, 26 Jun 2020 22:31:53: 3000000 INFO @ Fri, 26 Jun 2020 22:31:56: 16000000 INFO @ Fri, 26 Jun 2020 22:31:57: 9000000 INFO @ Fri, 26 Jun 2020 22:31:59: 4000000 INFO @ Fri, 26 Jun 2020 22:32:01: 17000000 INFO @ Fri, 26 Jun 2020 22:32:02: 10000000 INFO @ Fri, 26 Jun 2020 22:32:04: 5000000 INFO @ Fri, 26 Jun 2020 22:32:06: 18000000 INFO @ Fri, 26 Jun 2020 22:32:07: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:32:07: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:32:07: #1 total tags in treatment: 18155755 INFO @ Fri, 26 Jun 2020 22:32:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:32:07: #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 22:32:07: #1 tags after filtering in treatment: 18155755 INFO @ Fri, 26 Jun 2020 22:32:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:32:07: #1 finished! INFO @ Fri, 26 Jun 2020 22:32:07: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:32:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:32:08: 11000000 INFO @ Fri, 26 Jun 2020 22:32:08: #2 number of paired peaks: 261 WARNING @ Fri, 26 Jun 2020 22:32:08: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Fri, 26 Jun 2020 22:32:08: start model_add_line... INFO @ Fri, 26 Jun 2020 22:32:08: start X-correlation... INFO @ Fri, 26 Jun 2020 22:32:08: end of X-cor INFO @ Fri, 26 Jun 2020 22:32:08: #2 finished! INFO @ Fri, 26 Jun 2020 22:32:08: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:32:08: #2 alternative fragment length(s) may be 1,48,545 bps INFO @ Fri, 26 Jun 2020 22:32:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.05_model.r WARNING @ Fri, 26 Jun 2020 22:32:08: #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 22:32:08: #2 You may need to consider one of the other alternative d(s): 1,48,545 WARNING @ Fri, 26 Jun 2020 22:32:08: #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 22:32:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:32:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:32:10: 6000000 INFO @ Fri, 26 Jun 2020 22:32:14: 12000000 INFO @ Fri, 26 Jun 2020 22:32:16: 7000000 INFO @ Fri, 26 Jun 2020 22:32:19: 13000000 INFO @ Fri, 26 Jun 2020 22:32:21: 8000000 INFO @ Fri, 26 Jun 2020 22:32:25: 14000000 INFO @ Fri, 26 Jun 2020 22:32:27: 9000000 INFO @ Fri, 26 Jun 2020 22:32:30: 15000000 INFO @ Fri, 26 Jun 2020 22:32:32: 10000000 INFO @ Fri, 26 Jun 2020 22:32:36: 16000000 INFO @ Fri, 26 Jun 2020 22:32:38: 11000000 INFO @ Fri, 26 Jun 2020 22:32:38: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:32:42: 17000000 INFO @ Fri, 26 Jun 2020 22:32:43: 12000000 INFO @ Fri, 26 Jun 2020 22:32:47: 18000000 INFO @ Fri, 26 Jun 2020 22:32:48: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:32:48: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:32:48: #1 total tags in treatment: 18155755 INFO @ Fri, 26 Jun 2020 22:32:48: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:32:48: #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 22:32:49: #1 tags after filtering in treatment: 18155755 INFO @ Fri, 26 Jun 2020 22:32:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:32:49: #1 finished! INFO @ Fri, 26 Jun 2020 22:32:49: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:32:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:32:49: 13000000 INFO @ Fri, 26 Jun 2020 22:32:50: #2 number of paired peaks: 261 WARNING @ Fri, 26 Jun 2020 22:32:50: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Fri, 26 Jun 2020 22:32:50: start model_add_line... INFO @ Fri, 26 Jun 2020 22:32:50: start X-correlation... INFO @ Fri, 26 Jun 2020 22:32:50: end of X-cor INFO @ Fri, 26 Jun 2020 22:32:50: #2 finished! INFO @ Fri, 26 Jun 2020 22:32:50: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:32:50: #2 alternative fragment length(s) may be 1,48,545 bps INFO @ Fri, 26 Jun 2020 22:32:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.10_model.r WARNING @ Fri, 26 Jun 2020 22:32:50: #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 22:32:50: #2 You may need to consider one of the other alternative d(s): 1,48,545 WARNING @ Fri, 26 Jun 2020 22:32:50: #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 22:32:50: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:32:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:32:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:32:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:32:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.05_summits.bed INFO @ Fri, 26 Jun 2020 22:32:52: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:32:54: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:33:00: 15000000 INFO @ Fri, 26 Jun 2020 22:33:05: 16000000 INFO @ Fri, 26 Jun 2020 22:33:11: 17000000 INFO @ Fri, 26 Jun 2020 22:33:17: 18000000 INFO @ Fri, 26 Jun 2020 22:33:18: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:33:18: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:33:18: #1 total tags in treatment: 18155755 INFO @ Fri, 26 Jun 2020 22:33:18: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:33:18: #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 22:33:18: #1 tags after filtering in treatment: 18155755 INFO @ Fri, 26 Jun 2020 22:33:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:33:18: #1 finished! INFO @ Fri, 26 Jun 2020 22:33:18: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:33:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:33:19: #2 number of paired peaks: 261 WARNING @ Fri, 26 Jun 2020 22:33:19: Fewer paired peaks (261) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 261 pairs to build model! INFO @ Fri, 26 Jun 2020 22:33:19: start model_add_line... INFO @ Fri, 26 Jun 2020 22:33:20: start X-correlation... INFO @ Fri, 26 Jun 2020 22:33:20: end of X-cor INFO @ Fri, 26 Jun 2020 22:33:20: #2 finished! INFO @ Fri, 26 Jun 2020 22:33:20: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:33:20: #2 alternative fragment length(s) may be 1,48,545 bps INFO @ Fri, 26 Jun 2020 22:33:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.20_model.r WARNING @ Fri, 26 Jun 2020 22:33:20: #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 22:33:20: #2 You may need to consider one of the other alternative d(s): 1,48,545 WARNING @ Fri, 26 Jun 2020 22:33:20: #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 22:33:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:33:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:33:21: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:33:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:33:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:33:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.10_summits.bed INFO @ Fri, 26 Jun 2020 22:33:36: 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 22:33:52: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:34:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:34:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:34:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495123/SRX495123.20_summits.bed INFO @ Fri, 26 Jun 2020 22:34:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling