Job ID = 6459893 SRX = SRX969925 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:34:13 prefetch.2.10.7: 1) Downloading 'SRR1931641'... 2020-06-21T13:34:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:44:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:44:40 prefetch.2.10.7: 1) 'SRR1931641' was downloaded successfully Read 43281024 spots for SRR1931641/SRR1931641.sra Written 43281024 spots for SRR1931641/SRR1931641.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: 00:12:31 43281024 reads; of these: 43281024 (100.00%) were unpaired; of these: 2312906 (5.34%) aligned 0 times 25857980 (59.74%) aligned exactly 1 time 15110138 (34.91%) aligned >1 times 94.66% overall alignment rate Time searching: 00:12:31 Overall time: 00:12:31 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 20 files... [bam_rmdupse_core] 13363689 / 40968118 = 0.3262 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 @ Sun, 21 Jun 2020 23:08:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.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 @ Sun, 21 Jun 2020 23:08:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:08:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:08:28: 1000000 INFO @ Sun, 21 Jun 2020 23:08:33: 2000000 INFO @ Sun, 21 Jun 2020 23:08:38: 3000000 INFO @ Sun, 21 Jun 2020 23:08:43: 4000000 INFO @ Sun, 21 Jun 2020 23:08:48: 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 @ Sun, 21 Jun 2020 23:08:53: 6000000 INFO @ Sun, 21 Jun 2020 23:08:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.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 @ Sun, 21 Jun 2020 23:08:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:08:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:08:58: 7000000 INFO @ Sun, 21 Jun 2020 23:08:58: 1000000 INFO @ Sun, 21 Jun 2020 23:09:03: 8000000 INFO @ Sun, 21 Jun 2020 23:09:03: 2000000 INFO @ Sun, 21 Jun 2020 23:09:08: 9000000 INFO @ Sun, 21 Jun 2020 23:09:08: 3000000 INFO @ Sun, 21 Jun 2020 23:09:13: 10000000 INFO @ Sun, 21 Jun 2020 23:09:13: 4000000 INFO @ Sun, 21 Jun 2020 23:09:18: 11000000 INFO @ Sun, 21 Jun 2020 23:09:18: 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 @ Sun, 21 Jun 2020 23:09:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.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 @ Sun, 21 Jun 2020 23:09:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 23:09:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 23:09:23: 12000000 INFO @ Sun, 21 Jun 2020 23:09:24: 6000000 INFO @ Sun, 21 Jun 2020 23:09:28: 13000000 INFO @ Sun, 21 Jun 2020 23:09:28: 1000000 INFO @ Sun, 21 Jun 2020 23:09:29: 7000000 INFO @ Sun, 21 Jun 2020 23:09:34: 14000000 INFO @ Sun, 21 Jun 2020 23:09:34: 2000000 INFO @ Sun, 21 Jun 2020 23:09:34: 8000000 INFO @ Sun, 21 Jun 2020 23:09:39: 15000000 INFO @ Sun, 21 Jun 2020 23:09:39: 3000000 INFO @ Sun, 21 Jun 2020 23:09:39: 9000000 INFO @ Sun, 21 Jun 2020 23:09:44: 16000000 INFO @ Sun, 21 Jun 2020 23:09:44: 4000000 INFO @ Sun, 21 Jun 2020 23:09:45: 10000000 INFO @ Sun, 21 Jun 2020 23:09:49: 17000000 INFO @ Sun, 21 Jun 2020 23:09:49: 5000000 INFO @ Sun, 21 Jun 2020 23:09:50: 11000000 INFO @ Sun, 21 Jun 2020 23:09:54: 18000000 INFO @ Sun, 21 Jun 2020 23:09:55: 6000000 INFO @ Sun, 21 Jun 2020 23:09:55: 12000000 INFO @ Sun, 21 Jun 2020 23:10:00: 19000000 INFO @ Sun, 21 Jun 2020 23:10:00: 7000000 INFO @ Sun, 21 Jun 2020 23:10:00: 13000000 INFO @ Sun, 21 Jun 2020 23:10:05: 20000000 INFO @ Sun, 21 Jun 2020 23:10:05: 8000000 INFO @ Sun, 21 Jun 2020 23:10:05: 14000000 INFO @ Sun, 21 Jun 2020 23:10:10: 21000000 INFO @ Sun, 21 Jun 2020 23:10:10: 15000000 INFO @ Sun, 21 Jun 2020 23:10:10: 9000000 INFO @ Sun, 21 Jun 2020 23:10:15: 22000000 INFO @ Sun, 21 Jun 2020 23:10:16: 16000000 INFO @ Sun, 21 Jun 2020 23:10:16: 10000000 INFO @ Sun, 21 Jun 2020 23:10:21: 17000000 INFO @ Sun, 21 Jun 2020 23:10:21: 23000000 INFO @ Sun, 21 Jun 2020 23:10:21: 11000000 INFO @ Sun, 21 Jun 2020 23:10:26: 18000000 INFO @ Sun, 21 Jun 2020 23:10:26: 24000000 INFO @ Sun, 21 Jun 2020 23:10:26: 12000000 INFO @ Sun, 21 Jun 2020 23:10:31: 19000000 INFO @ Sun, 21 Jun 2020 23:10:31: 25000000 INFO @ Sun, 21 Jun 2020 23:10:31: 13000000 INFO @ Sun, 21 Jun 2020 23:10:36: 20000000 INFO @ Sun, 21 Jun 2020 23:10:36: 26000000 INFO @ Sun, 21 Jun 2020 23:10:36: 14000000 INFO @ Sun, 21 Jun 2020 23:10:41: 21000000 INFO @ Sun, 21 Jun 2020 23:10:42: 15000000 INFO @ Sun, 21 Jun 2020 23:10:42: 27000000 INFO @ Sun, 21 Jun 2020 23:10:45: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 23:10:45: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 23:10:45: #1 total tags in treatment: 27604429 INFO @ Sun, 21 Jun 2020 23:10:45: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:10:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 23:10:46: #1 tags after filtering in treatment: 27604429 INFO @ Sun, 21 Jun 2020 23:10:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:10:46: #1 finished! INFO @ Sun, 21 Jun 2020 23:10:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:10:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:10:47: 22000000 INFO @ Sun, 21 Jun 2020 23:10:47: 16000000 INFO @ Sun, 21 Jun 2020 23:10:48: #2 number of paired peaks: 677 WARNING @ Sun, 21 Jun 2020 23:10:48: Fewer paired peaks (677) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 677 pairs to build model! INFO @ Sun, 21 Jun 2020 23:10:48: start model_add_line... INFO @ Sun, 21 Jun 2020 23:10:48: start X-correlation... INFO @ Sun, 21 Jun 2020 23:10:48: end of X-cor INFO @ Sun, 21 Jun 2020 23:10:48: #2 finished! INFO @ Sun, 21 Jun 2020 23:10:48: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 23:10:48: #2 alternative fragment length(s) may be 1 bps INFO @ Sun, 21 Jun 2020 23:10:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.05_model.r WARNING @ Sun, 21 Jun 2020 23:10:48: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 23:10:48: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sun, 21 Jun 2020 23:10:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 23:10:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:10:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:10:52: 17000000 INFO @ Sun, 21 Jun 2020 23:10:52: 23000000 INFO @ Sun, 21 Jun 2020 23:10:57: 18000000 INFO @ Sun, 21 Jun 2020 23:10:57: 24000000 INFO @ Sun, 21 Jun 2020 23:11:03: 19000000 INFO @ Sun, 21 Jun 2020 23:11:03: 25000000 INFO @ Sun, 21 Jun 2020 23:11:08: 20000000 INFO @ Sun, 21 Jun 2020 23:11:08: 26000000 INFO @ Sun, 21 Jun 2020 23:11:13: 21000000 INFO @ Sun, 21 Jun 2020 23:11:13: 27000000 INFO @ Sun, 21 Jun 2020 23:11:16: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 23:11:16: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 23:11:16: #1 total tags in treatment: 27604429 INFO @ Sun, 21 Jun 2020 23:11:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:11:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 23:11:17: #1 tags after filtering in treatment: 27604429 INFO @ Sun, 21 Jun 2020 23:11:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:11:17: #1 finished! INFO @ Sun, 21 Jun 2020 23:11:17: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:11:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:11:19: 22000000 INFO @ Sun, 21 Jun 2020 23:11:19: #2 number of paired peaks: 677 WARNING @ Sun, 21 Jun 2020 23:11:19: Fewer paired peaks (677) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 677 pairs to build model! INFO @ Sun, 21 Jun 2020 23:11:19: start model_add_line... INFO @ Sun, 21 Jun 2020 23:11:19: start X-correlation... INFO @ Sun, 21 Jun 2020 23:11:19: end of X-cor INFO @ Sun, 21 Jun 2020 23:11:19: #2 finished! INFO @ Sun, 21 Jun 2020 23:11:19: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 23:11:19: #2 alternative fragment length(s) may be 1 bps INFO @ Sun, 21 Jun 2020 23:11:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.10_model.r WARNING @ Sun, 21 Jun 2020 23:11:19: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 23:11:19: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sun, 21 Jun 2020 23:11:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 23:11:19: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:11:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:11:24: 23000000 INFO @ Sun, 21 Jun 2020 23:11:29: 24000000 INFO @ Sun, 21 Jun 2020 23:11:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:11:34: 25000000 INFO @ Sun, 21 Jun 2020 23:11:39: 26000000 INFO @ Sun, 21 Jun 2020 23:11:44: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 23:11:48: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 23:11:48: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 23:11:48: #1 total tags in treatment: 27604429 INFO @ Sun, 21 Jun 2020 23:11:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 23:11:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 23:11:49: #1 tags after filtering in treatment: 27604429 INFO @ Sun, 21 Jun 2020 23:11:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 23:11:49: #1 finished! INFO @ Sun, 21 Jun 2020 23:11:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 23:11:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 23:11:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.05_peaks.xls INFO @ Sun, 21 Jun 2020 23:11:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:11:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.05_summits.bed INFO @ Sun, 21 Jun 2020 23:11:50: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:11:50: #2 number of paired peaks: 677 WARNING @ Sun, 21 Jun 2020 23:11:50: Fewer paired peaks (677) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 677 pairs to build model! INFO @ Sun, 21 Jun 2020 23:11:50: start model_add_line... INFO @ Sun, 21 Jun 2020 23:11:51: start X-correlation... INFO @ Sun, 21 Jun 2020 23:11:51: end of X-cor INFO @ Sun, 21 Jun 2020 23:11:51: #2 finished! INFO @ Sun, 21 Jun 2020 23:11:51: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 23:11:51: #2 alternative fragment length(s) may be 1 bps INFO @ Sun, 21 Jun 2020 23:11:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.20_model.r WARNING @ Sun, 21 Jun 2020 23:11:51: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 23:11:51: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Sun, 21 Jun 2020 23:11:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 23:11:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 23:11:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 23:12:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 23:12:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.10_peaks.xls INFO @ Sun, 21 Jun 2020 23:12:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:12:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.10_summits.bed INFO @ Sun, 21 Jun 2020 23:12:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 23:12:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 23:12:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.20_peaks.xls INFO @ Sun, 21 Jun 2020 23:12:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 23:12:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969925/SRX969925.20_summits.bed INFO @ Sun, 21 Jun 2020 23:12:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling