Job ID = 6454408 SRX = SRX2035280 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:03:49 prefetch.2.10.7: 1) Downloading 'SRR4044404'... 2020-06-21T09:03:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:07:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:07:18 prefetch.2.10.7: 1) 'SRR4044404' was downloaded successfully 2020-06-21T09:07:18 prefetch.2.10.7: 'SRR4044404' has 0 unresolved dependencies Read 26849084 spots for SRR4044404/SRR4044404.sra Written 26849084 spots for SRR4044404/SRR4044404.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: 00:11:10 26849084 reads; of these: 26849084 (100.00%) were unpaired; of these: 1146314 (4.27%) aligned 0 times 19269365 (71.77%) aligned exactly 1 time 6433405 (23.96%) aligned >1 times 95.73% overall alignment rate Time searching: 00:11:10 Overall time: 00:11:10 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 12 files... [bam_rmdupse_core] 4887872 / 25702770 = 0.1902 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 18:27:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.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 18:27:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:27:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:27:11: 1000000 INFO @ Sun, 21 Jun 2020 18:27:17: 2000000 INFO @ Sun, 21 Jun 2020 18:27:24: 3000000 INFO @ Sun, 21 Jun 2020 18:27:30: 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 @ Sun, 21 Jun 2020 18:27:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.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 18:27:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:27:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:27:37: 5000000 INFO @ Sun, 21 Jun 2020 18:27:42: 1000000 INFO @ Sun, 21 Jun 2020 18:27:45: 6000000 INFO @ Sun, 21 Jun 2020 18:27:50: 2000000 INFO @ Sun, 21 Jun 2020 18:27:53: 7000000 INFO @ Sun, 21 Jun 2020 18:27:58: 3000000 INFO @ Sun, 21 Jun 2020 18:28:00: 8000000 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 18:28:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.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 18:28:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:28:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:28:05: 4000000 INFO @ Sun, 21 Jun 2020 18:28:08: 9000000 INFO @ Sun, 21 Jun 2020 18:28:14: 1000000 INFO @ Sun, 21 Jun 2020 18:28:14: 5000000 INFO @ Sun, 21 Jun 2020 18:28:17: 10000000 INFO @ Sun, 21 Jun 2020 18:28:22: 6000000 INFO @ Sun, 21 Jun 2020 18:28:22: 2000000 INFO @ Sun, 21 Jun 2020 18:28:25: 11000000 INFO @ Sun, 21 Jun 2020 18:28:30: 7000000 INFO @ Sun, 21 Jun 2020 18:28:31: 3000000 INFO @ Sun, 21 Jun 2020 18:28:33: 12000000 INFO @ Sun, 21 Jun 2020 18:28:38: 8000000 INFO @ Sun, 21 Jun 2020 18:28:40: 4000000 INFO @ Sun, 21 Jun 2020 18:28:42: 13000000 INFO @ Sun, 21 Jun 2020 18:28:46: 9000000 INFO @ Sun, 21 Jun 2020 18:28:49: 5000000 INFO @ Sun, 21 Jun 2020 18:28:50: 14000000 INFO @ Sun, 21 Jun 2020 18:28:54: 10000000 INFO @ Sun, 21 Jun 2020 18:28:58: 15000000 INFO @ Sun, 21 Jun 2020 18:28:58: 6000000 INFO @ Sun, 21 Jun 2020 18:29:03: 11000000 INFO @ Sun, 21 Jun 2020 18:29:06: 16000000 INFO @ Sun, 21 Jun 2020 18:29:07: 7000000 INFO @ Sun, 21 Jun 2020 18:29:11: 12000000 INFO @ Sun, 21 Jun 2020 18:29:15: 17000000 INFO @ Sun, 21 Jun 2020 18:29:15: 8000000 INFO @ Sun, 21 Jun 2020 18:29:19: 13000000 INFO @ Sun, 21 Jun 2020 18:29:23: 18000000 INFO @ Sun, 21 Jun 2020 18:29:24: 9000000 INFO @ Sun, 21 Jun 2020 18:29:27: 14000000 INFO @ Sun, 21 Jun 2020 18:29:31: 19000000 INFO @ Sun, 21 Jun 2020 18:29:33: 10000000 INFO @ Sun, 21 Jun 2020 18:29:35: 15000000 INFO @ Sun, 21 Jun 2020 18:29:39: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:29:42: 11000000 INFO @ Sun, 21 Jun 2020 18:29:43: 16000000 INFO @ Sun, 21 Jun 2020 18:29:46: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 18:29:46: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 18:29:46: #1 total tags in treatment: 20814898 INFO @ Sun, 21 Jun 2020 18:29:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:29:46: #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 18:29:47: #1 tags after filtering in treatment: 20814896 INFO @ Sun, 21 Jun 2020 18:29:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:29:47: #1 finished! INFO @ Sun, 21 Jun 2020 18:29:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:29:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:29:48: #2 number of paired peaks: 733 WARNING @ Sun, 21 Jun 2020 18:29:48: Fewer paired peaks (733) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 733 pairs to build model! INFO @ Sun, 21 Jun 2020 18:29:48: start model_add_line... INFO @ Sun, 21 Jun 2020 18:29:49: start X-correlation... INFO @ Sun, 21 Jun 2020 18:29:49: end of X-cor INFO @ Sun, 21 Jun 2020 18:29:49: #2 finished! INFO @ Sun, 21 Jun 2020 18:29:49: #2 predicted fragment length is 120 bps INFO @ Sun, 21 Jun 2020 18:29:49: #2 alternative fragment length(s) may be 120 bps INFO @ Sun, 21 Jun 2020 18:29:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.05_model.r WARNING @ Sun, 21 Jun 2020 18:29:49: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:29:49: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Sun, 21 Jun 2020 18:29:49: #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 18:29:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:29:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:29:51: 12000000 INFO @ Sun, 21 Jun 2020 18:29:52: 17000000 INFO @ Sun, 21 Jun 2020 18:29:59: 13000000 INFO @ Sun, 21 Jun 2020 18:30:00: 18000000 INFO @ Sun, 21 Jun 2020 18:30:08: 19000000 INFO @ Sun, 21 Jun 2020 18:30:08: 14000000 INFO @ Sun, 21 Jun 2020 18:30:16: 20000000 INFO @ Sun, 21 Jun 2020 18:30:17: 15000000 INFO @ Sun, 21 Jun 2020 18:30:22: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 18:30:22: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 18:30:22: #1 total tags in treatment: 20814898 INFO @ Sun, 21 Jun 2020 18:30:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:30:22: #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 18:30:23: #1 tags after filtering in treatment: 20814896 INFO @ Sun, 21 Jun 2020 18:30:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:30:23: #1 finished! INFO @ Sun, 21 Jun 2020 18:30:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:30:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:30:24: #2 number of paired peaks: 733 WARNING @ Sun, 21 Jun 2020 18:30:24: Fewer paired peaks (733) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 733 pairs to build model! INFO @ Sun, 21 Jun 2020 18:30:24: start model_add_line... INFO @ Sun, 21 Jun 2020 18:30:25: start X-correlation... INFO @ Sun, 21 Jun 2020 18:30:25: end of X-cor INFO @ Sun, 21 Jun 2020 18:30:25: #2 finished! INFO @ Sun, 21 Jun 2020 18:30:25: #2 predicted fragment length is 120 bps INFO @ Sun, 21 Jun 2020 18:30:25: #2 alternative fragment length(s) may be 120 bps INFO @ Sun, 21 Jun 2020 18:30:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.10_model.r WARNING @ Sun, 21 Jun 2020 18:30:25: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:30:25: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Sun, 21 Jun 2020 18:30:25: #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 18:30:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:30:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:30:26: 16000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:30:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:30:34: 17000000 INFO @ Sun, 21 Jun 2020 18:30:43: 18000000 INFO @ Sun, 21 Jun 2020 18:30:51: 19000000 INFO @ Sun, 21 Jun 2020 18:30:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:30:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:30:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.05_summits.bed INFO @ Sun, 21 Jun 2020 18:30:54: Done! pass1 - making usageList (816 chroms): 3 millis pass2 - checking and writing primary data (12753 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:30:59: 20000000 INFO @ Sun, 21 Jun 2020 18:31:06: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 18:31:06: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 18:31:06: #1 total tags in treatment: 20814898 INFO @ Sun, 21 Jun 2020 18:31:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:31:06: #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 18:31:07: #1 tags after filtering in treatment: 20814896 INFO @ Sun, 21 Jun 2020 18:31:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:31:07: #1 finished! INFO @ Sun, 21 Jun 2020 18:31:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:31:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:31:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:31:08: #2 number of paired peaks: 733 WARNING @ Sun, 21 Jun 2020 18:31:08: Fewer paired peaks (733) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 733 pairs to build model! INFO @ Sun, 21 Jun 2020 18:31:08: start model_add_line... INFO @ Sun, 21 Jun 2020 18:31:08: start X-correlation... INFO @ Sun, 21 Jun 2020 18:31:09: end of X-cor INFO @ Sun, 21 Jun 2020 18:31:09: #2 finished! INFO @ Sun, 21 Jun 2020 18:31:09: #2 predicted fragment length is 120 bps INFO @ Sun, 21 Jun 2020 18:31:09: #2 alternative fragment length(s) may be 120 bps INFO @ Sun, 21 Jun 2020 18:31:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.20_model.r WARNING @ Sun, 21 Jun 2020 18:31:09: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:31:09: #2 You may need to consider one of the other alternative d(s): 120 WARNING @ Sun, 21 Jun 2020 18:31:09: #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 18:31:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:31:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:31:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:31:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:31:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.10_summits.bed INFO @ Sun, 21 Jun 2020 18:31:30: Done! pass1 - making usageList (677 chroms): 2 millis pass2 - checking and writing primary data (8395 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:31:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:32:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:32:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:32:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2035280/SRX2035280.20_summits.bed INFO @ Sun, 21 Jun 2020 18:32:17: Done! pass1 - making usageList (502 chroms): 2 millis pass2 - checking and writing primary data (5136 records, 4 fields): 21 millis CompletedMACS2peakCalling