Job ID = 6497533 SRX = SRX495123 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:46:43 prefetch.2.10.7: 1) Downloading 'SRR1198655'... 2020-06-25T21:46:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:48:46 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:48:46 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: 00:04:51 22970231 reads; of these: 22970231 (100.00%) were unpaired; of these: 2517571 (10.96%) aligned 0 times 16805798 (73.16%) aligned exactly 1 time 3646862 (15.88%) aligned >1 times 89.04% overall alignment rate Time searching: 00:04:51 Overall time: 00:04:51 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] 2297243 / 20452660 = 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 07:01:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495123/SRX495123.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495123/SRX495123.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495123/SRX495123.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:01:52: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:01:52: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:01:57: 1000000 INFO @ Fri, 26 Jun 2020 07:02:02: 2000000 INFO @ Fri, 26 Jun 2020 07:02:07: 3000000 INFO @ Fri, 26 Jun 2020 07:02:12: 4000000 INFO @ Fri, 26 Jun 2020 07:02:17: 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 07:02:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495123/SRX495123.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495123/SRX495123.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495123/SRX495123.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:02:22: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:02:22: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:02:23: 6000000 INFO @ Fri, 26 Jun 2020 07:02:28: 1000000 INFO @ Fri, 26 Jun 2020 07:02:28: 7000000 INFO @ Fri, 26 Jun 2020 07:02:33: 2000000 INFO @ Fri, 26 Jun 2020 07:02:33: 8000000 INFO @ Fri, 26 Jun 2020 07:02:39: 9000000 INFO @ Fri, 26 Jun 2020 07:02:39: 3000000 INFO @ Fri, 26 Jun 2020 07:02:44: 10000000 INFO @ Fri, 26 Jun 2020 07:02:45: 4000000 INFO @ Fri, 26 Jun 2020 07:02:50: 11000000 BedGraph に変換中... INFO @ Fri, 26 Jun 2020 07:02:50: 5000000 INFO @ Fri, 26 Jun 2020 07:02:55: 12000000 INFO @ Fri, 26 Jun 2020 07:02:56: 6000000 INFO @ Fri, 26 Jun 2020 07:03:01: 13000000 INFO @ Fri, 26 Jun 2020 07:03:01: 7000000 INFO @ Fri, 26 Jun 2020 07:03:06: 14000000 INFO @ Fri, 26 Jun 2020 07:03:07: 8000000 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 07:03:12: 15000000 INFO @ Fri, 26 Jun 2020 07:03:12: 9000000 INFO @ Fri, 26 Jun 2020 07:03:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495123/SRX495123.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495123/SRX495123.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495123/SRX495123.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:03:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:03:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:03:17: 16000000 INFO @ Fri, 26 Jun 2020 07:03:18: 10000000 INFO @ Fri, 26 Jun 2020 07:03:19: 1000000 INFO @ Fri, 26 Jun 2020 07:03:23: 17000000 INFO @ Fri, 26 Jun 2020 07:03:24: 11000000 INFO @ Fri, 26 Jun 2020 07:03:24: 2000000 INFO @ Fri, 26 Jun 2020 07:03:29: 18000000 INFO @ Fri, 26 Jun 2020 07:03:30: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:03:30: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:03:30: #1 total tags in treatment: 18155417 INFO @ Fri, 26 Jun 2020 07:03:30: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:03:30: #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 07:03:30: 3000000 INFO @ Fri, 26 Jun 2020 07:03:30: #1 tags after filtering in treatment: 18155417 INFO @ Fri, 26 Jun 2020 07:03:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:03:30: #1 finished! INFO @ Fri, 26 Jun 2020 07:03:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:03:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:03:30: 12000000 INFO @ Fri, 26 Jun 2020 07:03:31: #2 number of paired peaks: 260 WARNING @ Fri, 26 Jun 2020 07:03:31: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Fri, 26 Jun 2020 07:03:31: start model_add_line... INFO @ Fri, 26 Jun 2020 07:03:31: start X-correlation... INFO @ Fri, 26 Jun 2020 07:03:31: end of X-cor INFO @ Fri, 26 Jun 2020 07:03:31: #2 finished! INFO @ Fri, 26 Jun 2020 07:03:31: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:03:31: #2 alternative fragment length(s) may be 1,48,544 bps INFO @ Fri, 26 Jun 2020 07:03:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495123/SRX495123.05_model.r WARNING @ Fri, 26 Jun 2020 07:03:31: #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 07:03:31: #2 You may need to consider one of the other alternative d(s): 1,48,544 WARNING @ Fri, 26 Jun 2020 07:03:31: #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 07:03:31: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:03:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:03:35: 4000000 INFO @ Fri, 26 Jun 2020 07:03:36: 13000000 INFO @ Fri, 26 Jun 2020 07:03:41: 5000000 INFO @ Fri, 26 Jun 2020 07:03:42: 14000000 INFO @ Fri, 26 Jun 2020 07:03:47: 6000000 INFO @ Fri, 26 Jun 2020 07:03:49: 15000000 INFO @ Fri, 26 Jun 2020 07:03:52: 7000000 INFO @ Fri, 26 Jun 2020 07:03:55: 16000000 INFO @ Fri, 26 Jun 2020 07:03:58: 8000000 INFO @ Fri, 26 Jun 2020 07:03:58: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:04:01: 17000000 INFO @ Fri, 26 Jun 2020 07:04:04: 9000000 INFO @ Fri, 26 Jun 2020 07:04:07: 18000000 INFO @ Fri, 26 Jun 2020 07:04:08: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:04:08: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:04:08: #1 total tags in treatment: 18155417 INFO @ Fri, 26 Jun 2020 07:04:08: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:04:08: #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 07:04:08: #1 tags after filtering in treatment: 18155417 INFO @ Fri, 26 Jun 2020 07:04:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:04:08: #1 finished! INFO @ Fri, 26 Jun 2020 07:04:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:04:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:04:09: 10000000 INFO @ Fri, 26 Jun 2020 07:04:10: #2 number of paired peaks: 260 WARNING @ Fri, 26 Jun 2020 07:04:10: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Fri, 26 Jun 2020 07:04:10: start model_add_line... INFO @ Fri, 26 Jun 2020 07:04:10: start X-correlation... INFO @ Fri, 26 Jun 2020 07:04:10: end of X-cor INFO @ Fri, 26 Jun 2020 07:04:10: #2 finished! INFO @ Fri, 26 Jun 2020 07:04:10: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:04:10: #2 alternative fragment length(s) may be 1,48,544 bps INFO @ Fri, 26 Jun 2020 07:04:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495123/SRX495123.10_model.r WARNING @ Fri, 26 Jun 2020 07:04:10: #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 07:04:10: #2 You may need to consider one of the other alternative d(s): 1,48,544 WARNING @ Fri, 26 Jun 2020 07:04:10: #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 07:04:10: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:04:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:04:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495123/SRX495123.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:04:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495123/SRX495123.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:04:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495123/SRX495123.05_summits.bed INFO @ Fri, 26 Jun 2020 07:04:10: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:04:15: 11000000 INFO @ Fri, 26 Jun 2020 07:04:20: 12000000 INFO @ Fri, 26 Jun 2020 07:04:25: 13000000 INFO @ Fri, 26 Jun 2020 07:04:30: 14000000 INFO @ Fri, 26 Jun 2020 07:04:35: 15000000 INFO @ Fri, 26 Jun 2020 07:04:36: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:04:41: 16000000 INFO @ Fri, 26 Jun 2020 07:04:46: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:04:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495123/SRX495123.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:04:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495123/SRX495123.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:04:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495123/SRX495123.10_summits.bed INFO @ Fri, 26 Jun 2020 07:04:49: Done! pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:04:51: 18000000 INFO @ Fri, 26 Jun 2020 07:04:52: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:04:52: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:04:52: #1 total tags in treatment: 18155417 INFO @ Fri, 26 Jun 2020 07:04:52: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:04:52: #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 07:04:52: #1 tags after filtering in treatment: 18155417 INFO @ Fri, 26 Jun 2020 07:04:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:04:52: #1 finished! INFO @ Fri, 26 Jun 2020 07:04:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:04:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:04:53: #2 number of paired peaks: 260 WARNING @ Fri, 26 Jun 2020 07:04:53: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Fri, 26 Jun 2020 07:04:53: start model_add_line... INFO @ Fri, 26 Jun 2020 07:04:53: start X-correlation... INFO @ Fri, 26 Jun 2020 07:04:53: end of X-cor INFO @ Fri, 26 Jun 2020 07:04:53: #2 finished! INFO @ Fri, 26 Jun 2020 07:04:53: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:04:53: #2 alternative fragment length(s) may be 1,48,544 bps INFO @ Fri, 26 Jun 2020 07:04:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495123/SRX495123.20_model.r WARNING @ Fri, 26 Jun 2020 07:04:53: #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 07:04:53: #2 You may need to consider one of the other alternative d(s): 1,48,544 WARNING @ Fri, 26 Jun 2020 07:04:53: #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 07:04:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:04:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:05:20: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:05:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495123/SRX495123.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:05:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495123/SRX495123.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:05:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495123/SRX495123.20_summits.bed INFO @ Fri, 26 Jun 2020 07:05:42: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。