Job ID = 6508848 SRX = SRX495221 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:57:14 prefetch.2.10.7: 1) Downloading 'SRR1198726'... 2020-06-26T14:57:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:58:54 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:58:54 prefetch.2.10.7: 1) 'SRR1198726' was downloaded successfully Read 18189117 spots for SRR1198726/SRR1198726.sra Written 18189117 spots for SRR1198726/SRR1198726.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: 00:05:01 18189117 reads; of these: 18189117 (100.00%) were unpaired; of these: 771597 (4.24%) aligned 0 times 12560215 (69.05%) aligned exactly 1 time 4857305 (26.70%) aligned >1 times 95.76% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3620473 / 17417520 = 0.2079 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 @ Sat, 27 Jun 2020 00:09:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sat, 27 Jun 2020 00:09:18: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:09:18: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:09:24: 1000000 INFO @ Sat, 27 Jun 2020 00:09:30: 2000000 INFO @ Sat, 27 Jun 2020 00:09:36: 3000000 INFO @ Sat, 27 Jun 2020 00:09:42: 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 @ Sat, 27 Jun 2020 00:09:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sat, 27 Jun 2020 00:09:48: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:09:48: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:09:48: 5000000 INFO @ Sat, 27 Jun 2020 00:09:54: 1000000 INFO @ Sat, 27 Jun 2020 00:09:55: 6000000 INFO @ Sat, 27 Jun 2020 00:10:00: 2000000 INFO @ Sat, 27 Jun 2020 00:10:01: 7000000 INFO @ Sat, 27 Jun 2020 00:10:07: 3000000 INFO @ Sat, 27 Jun 2020 00:10:07: 8000000 INFO @ Sat, 27 Jun 2020 00:10:13: 9000000 INFO @ Sat, 27 Jun 2020 00:10:13: 4000000 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 @ Sat, 27 Jun 2020 00:10:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sat, 27 Jun 2020 00:10:18: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:10:18: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:10:18: 10000000 INFO @ Sat, 27 Jun 2020 00:10:19: 5000000 INFO @ Sat, 27 Jun 2020 00:10:24: 1000000 INFO @ Sat, 27 Jun 2020 00:10:25: 11000000 INFO @ Sat, 27 Jun 2020 00:10:26: 6000000 INFO @ Sat, 27 Jun 2020 00:10:31: 12000000 INFO @ Sat, 27 Jun 2020 00:10:31: 2000000 INFO @ Sat, 27 Jun 2020 00:10:32: 7000000 INFO @ Sat, 27 Jun 2020 00:10:36: 13000000 INFO @ Sat, 27 Jun 2020 00:10:37: 3000000 INFO @ Sat, 27 Jun 2020 00:10:38: 8000000 INFO @ Sat, 27 Jun 2020 00:10:42: #1 tag size is determined as 44 bps INFO @ Sat, 27 Jun 2020 00:10:42: #1 tag size = 44 INFO @ Sat, 27 Jun 2020 00:10:42: #1 total tags in treatment: 13797047 INFO @ Sat, 27 Jun 2020 00:10:42: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:10:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:10:42: #1 tags after filtering in treatment: 13796975 INFO @ Sat, 27 Jun 2020 00:10:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:10:42: #1 finished! INFO @ Sat, 27 Jun 2020 00:10:42: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:10:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:10:43: 4000000 INFO @ Sat, 27 Jun 2020 00:10:43: #2 number of paired peaks: 179 WARNING @ Sat, 27 Jun 2020 00:10:43: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Sat, 27 Jun 2020 00:10:43: start model_add_line... INFO @ Sat, 27 Jun 2020 00:10:43: start X-correlation... INFO @ Sat, 27 Jun 2020 00:10:43: end of X-cor INFO @ Sat, 27 Jun 2020 00:10:43: #2 finished! INFO @ Sat, 27 Jun 2020 00:10:43: #2 predicted fragment length is 3 bps INFO @ Sat, 27 Jun 2020 00:10:43: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sat, 27 Jun 2020 00:10:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.05_model.r WARNING @ Sat, 27 Jun 2020 00:10:43: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:10:43: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sat, 27 Jun 2020 00:10:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:10:43: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:10:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:10:44: 9000000 INFO @ Sat, 27 Jun 2020 00:10:49: 5000000 INFO @ Sat, 27 Jun 2020 00:10:50: 10000000 INFO @ Sat, 27 Jun 2020 00:10:55: 6000000 INFO @ Sat, 27 Jun 2020 00:10:57: 11000000 INFO @ Sat, 27 Jun 2020 00:11:01: 7000000 INFO @ Sat, 27 Jun 2020 00:11:03: 12000000 INFO @ Sat, 27 Jun 2020 00:11:07: 8000000 INFO @ Sat, 27 Jun 2020 00:11:09: 13000000 INFO @ Sat, 27 Jun 2020 00:11:12: 9000000 INFO @ Sat, 27 Jun 2020 00:11:14: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:11:14: #1 tag size is determined as 44 bps INFO @ Sat, 27 Jun 2020 00:11:14: #1 tag size = 44 INFO @ Sat, 27 Jun 2020 00:11:14: #1 total tags in treatment: 13797047 INFO @ Sat, 27 Jun 2020 00:11:14: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:11:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:11:15: #1 tags after filtering in treatment: 13796975 INFO @ Sat, 27 Jun 2020 00:11:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:11:15: #1 finished! INFO @ Sat, 27 Jun 2020 00:11:15: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:11:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:11:16: #2 number of paired peaks: 179 WARNING @ Sat, 27 Jun 2020 00:11:16: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Sat, 27 Jun 2020 00:11:16: start model_add_line... INFO @ Sat, 27 Jun 2020 00:11:16: start X-correlation... INFO @ Sat, 27 Jun 2020 00:11:16: end of X-cor INFO @ Sat, 27 Jun 2020 00:11:16: #2 finished! INFO @ Sat, 27 Jun 2020 00:11:16: #2 predicted fragment length is 3 bps INFO @ Sat, 27 Jun 2020 00:11:16: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sat, 27 Jun 2020 00:11:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.10_model.r WARNING @ Sat, 27 Jun 2020 00:11:16: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:11:16: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sat, 27 Jun 2020 00:11:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:11:16: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:11:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:11:18: 10000000 INFO @ Sat, 27 Jun 2020 00:11:24: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:11:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:11:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:11:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.05_summits.bed INFO @ Sat, 27 Jun 2020 00:11:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:11:30: 12000000 INFO @ Sat, 27 Jun 2020 00:11:35: 13000000 INFO @ Sat, 27 Jun 2020 00:11:40: #1 tag size is determined as 44 bps INFO @ Sat, 27 Jun 2020 00:11:40: #1 tag size = 44 INFO @ Sat, 27 Jun 2020 00:11:40: #1 total tags in treatment: 13797047 INFO @ Sat, 27 Jun 2020 00:11:40: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:11:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:11:40: #1 tags after filtering in treatment: 13796975 INFO @ Sat, 27 Jun 2020 00:11:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:11:40: #1 finished! INFO @ Sat, 27 Jun 2020 00:11:40: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:11:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:11:41: #2 number of paired peaks: 179 WARNING @ Sat, 27 Jun 2020 00:11:41: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Sat, 27 Jun 2020 00:11:41: start model_add_line... INFO @ Sat, 27 Jun 2020 00:11:41: start X-correlation... INFO @ Sat, 27 Jun 2020 00:11:41: end of X-cor INFO @ Sat, 27 Jun 2020 00:11:41: #2 finished! INFO @ Sat, 27 Jun 2020 00:11:41: #2 predicted fragment length is 3 bps INFO @ Sat, 27 Jun 2020 00:11:41: #2 alternative fragment length(s) may be 3,40 bps INFO @ Sat, 27 Jun 2020 00:11:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.20_model.r WARNING @ Sat, 27 Jun 2020 00:11:41: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:11:41: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Sat, 27 Jun 2020 00:11:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:11:41: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:11:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 27 Jun 2020 00:11:46: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:12:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:12:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:12:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.10_summits.bed INFO @ Sat, 27 Jun 2020 00:12:00: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:12:10: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:12:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:12:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:12:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495221/SRX495221.20_summits.bed INFO @ Sat, 27 Jun 2020 00:12:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling