Job ID = 6368651 SRX = SRX529211 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:20:51 prefetch.2.10.7: 1) Downloading 'SRR1265815'... 2020-06-16T00:20:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:23:13 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:23:13 prefetch.2.10.7: 1) 'SRR1265815' was downloaded successfully Read 19263987 spots for SRR1265815/SRR1265815.sra Written 19263987 spots for SRR1265815/SRR1265815.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: 00:03:31 19263987 reads; of these: 19263987 (100.00%) were unpaired; of these: 286034 (1.48%) aligned 0 times 15657755 (81.28%) aligned exactly 1 time 3320198 (17.24%) aligned >1 times 98.52% overall alignment rate Time searching: 00:03:32 Overall time: 00:03:32 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 8 files... [bam_rmdupse_core] 1890536 / 18977953 = 0.0996 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 @ Tue, 16 Jun 2020 09:32:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.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 @ Tue, 16 Jun 2020 09:32:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:41: 1000000 INFO @ Tue, 16 Jun 2020 09:32:46: 2000000 INFO @ Tue, 16 Jun 2020 09:32:51: 3000000 INFO @ Tue, 16 Jun 2020 09:32:57: 4000000 INFO @ Tue, 16 Jun 2020 09:33:02: 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 @ Tue, 16 Jun 2020 09:33:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.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 @ Tue, 16 Jun 2020 09:33:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:07: 6000000 INFO @ Tue, 16 Jun 2020 09:33:11: 1000000 INFO @ Tue, 16 Jun 2020 09:33:13: 7000000 INFO @ Tue, 16 Jun 2020 09:33:16: 2000000 INFO @ Tue, 16 Jun 2020 09:33:18: 8000000 INFO @ Tue, 16 Jun 2020 09:33:21: 3000000 INFO @ Tue, 16 Jun 2020 09:33:23: 9000000 INFO @ Tue, 16 Jun 2020 09:33:27: 4000000 INFO @ Tue, 16 Jun 2020 09:33:29: 10000000 INFO @ Tue, 16 Jun 2020 09:33:33: 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 @ Tue, 16 Jun 2020 09:33:34: 11000000 INFO @ Tue, 16 Jun 2020 09:33:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.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 @ Tue, 16 Jun 2020 09:33:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:38: 6000000 INFO @ Tue, 16 Jun 2020 09:33:40: 12000000 INFO @ Tue, 16 Jun 2020 09:33:41: 1000000 INFO @ Tue, 16 Jun 2020 09:33:44: 7000000 INFO @ Tue, 16 Jun 2020 09:33:45: 13000000 INFO @ Tue, 16 Jun 2020 09:33:46: 2000000 INFO @ Tue, 16 Jun 2020 09:33:49: 8000000 INFO @ Tue, 16 Jun 2020 09:33:51: 3000000 INFO @ Tue, 16 Jun 2020 09:33:51: 14000000 INFO @ Tue, 16 Jun 2020 09:33:55: 9000000 INFO @ Tue, 16 Jun 2020 09:33:56: 4000000 INFO @ Tue, 16 Jun 2020 09:33:57: 15000000 INFO @ Tue, 16 Jun 2020 09:34:00: 10000000 INFO @ Tue, 16 Jun 2020 09:34:01: 5000000 INFO @ Tue, 16 Jun 2020 09:34:02: 16000000 INFO @ Tue, 16 Jun 2020 09:34:05: 11000000 INFO @ Tue, 16 Jun 2020 09:34:06: 6000000 INFO @ Tue, 16 Jun 2020 09:34:08: 17000000 INFO @ Tue, 16 Jun 2020 09:34:08: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:34:08: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:34:08: #1 total tags in treatment: 17087417 INFO @ Tue, 16 Jun 2020 09:34:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:34:09: #1 tags after filtering in treatment: 17087417 INFO @ Tue, 16 Jun 2020 09:34:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:09: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:10: #2 number of paired peaks: 184 WARNING @ Tue, 16 Jun 2020 09:34:10: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:10: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:10: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:10: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:10: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:10: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:34:10: #2 alternative fragment length(s) may be 1,32,528,542,546,553 bps INFO @ Tue, 16 Jun 2020 09:34:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.05_model.r WARNING @ Tue, 16 Jun 2020 09:34:10: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:34:10: #2 You may need to consider one of the other alternative d(s): 1,32,528,542,546,553 WARNING @ Tue, 16 Jun 2020 09:34:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:34:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:11: 12000000 INFO @ Tue, 16 Jun 2020 09:34:11: 7000000 INFO @ Tue, 16 Jun 2020 09:34:16: 8000000 INFO @ Tue, 16 Jun 2020 09:34:17: 13000000 INFO @ Tue, 16 Jun 2020 09:34:22: 14000000 INFO @ Tue, 16 Jun 2020 09:34:22: 9000000 INFO @ Tue, 16 Jun 2020 09:34:27: 10000000 INFO @ Tue, 16 Jun 2020 09:34:27: 15000000 INFO @ Tue, 16 Jun 2020 09:34:32: 11000000 INFO @ Tue, 16 Jun 2020 09:34:33: 16000000 INFO @ Tue, 16 Jun 2020 09:34:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:34:37: 12000000 INFO @ Tue, 16 Jun 2020 09:34:38: 17000000 INFO @ Tue, 16 Jun 2020 09:34:39: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:34:39: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:34:39: #1 total tags in treatment: 17087417 INFO @ Tue, 16 Jun 2020 09:34:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:34:39: #1 tags after filtering in treatment: 17087417 INFO @ Tue, 16 Jun 2020 09:34:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:39: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:40: #2 number of paired peaks: 184 WARNING @ Tue, 16 Jun 2020 09:34:40: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:40: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:40: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:40: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:40: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:34:40: #2 alternative fragment length(s) may be 1,32,528,542,546,553 bps INFO @ Tue, 16 Jun 2020 09:34:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.10_model.r WARNING @ Tue, 16 Jun 2020 09:34:40: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:34:40: #2 You may need to consider one of the other alternative d(s): 1,32,528,542,546,553 WARNING @ Tue, 16 Jun 2020 09:34:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:34:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:42: 13000000 INFO @ Tue, 16 Jun 2020 09:34:48: 14000000 INFO @ Tue, 16 Jun 2020 09:34:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.05_summits.bed INFO @ Tue, 16 Jun 2020 09:34:49: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:34:53: 15000000 INFO @ Tue, 16 Jun 2020 09:34:58: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:35:03: 17000000 INFO @ Tue, 16 Jun 2020 09:35:03: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:35:03: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:35:03: #1 total tags in treatment: 17087417 INFO @ Tue, 16 Jun 2020 09:35:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:35:03: #1 tags after filtering in treatment: 17087417 INFO @ Tue, 16 Jun 2020 09:35:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:04: #2 number of paired peaks: 184 WARNING @ Tue, 16 Jun 2020 09:35:04: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:05: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:35:05: #2 alternative fragment length(s) may be 1,32,528,542,546,553 bps INFO @ Tue, 16 Jun 2020 09:35:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.20_model.r WARNING @ Tue, 16 Jun 2020 09:35:05: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:05: #2 You may need to consider one of the other alternative d(s): 1,32,528,542,546,553 WARNING @ Tue, 16 Jun 2020 09:35:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:35:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.10_summits.bed INFO @ Tue, 16 Jun 2020 09:35:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:35:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:35:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529211/SRX529211.20_summits.bed INFO @ Tue, 16 Jun 2020 09:35:44: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling