Job ID = 6454112 SRX = SRX1837288 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:59:34 prefetch.2.10.7: 1) Downloading 'SRR3657644'... 2020-06-21T08:59:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:02:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:02:56 prefetch.2.10.7: 1) 'SRR3657644' was downloaded successfully 2020-06-21T09:02:56 prefetch.2.10.7: 'SRR3657644' has 0 unresolved dependencies Read 27124521 spots for SRR3657644/SRR3657644.sra Written 27124521 spots for SRR3657644/SRR3657644.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: 00:09:02 27124521 reads; of these: 27124521 (100.00%) were unpaired; of these: 1527268 (5.63%) aligned 0 times 9046584 (33.35%) aligned exactly 1 time 16550669 (61.02%) aligned >1 times 94.37% overall alignment rate Time searching: 00:09:02 Overall time: 00:09:02 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 12 files... [bam_rmdupse_core] 9612043 / 25597253 = 0.3755 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 18:18:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.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 18:18:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:18:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:18:39: 1000000 INFO @ Sun, 21 Jun 2020 18:18:45: 2000000 INFO @ Sun, 21 Jun 2020 18:18:50: 3000000 INFO @ Sun, 21 Jun 2020 18:18:55: 4000000 INFO @ Sun, 21 Jun 2020 18:19:00: 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 18:19:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.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 18:19:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:05: 6000000 INFO @ Sun, 21 Jun 2020 18:19:10: 1000000 INFO @ Sun, 21 Jun 2020 18:19:11: 7000000 INFO @ Sun, 21 Jun 2020 18:19:16: 2000000 INFO @ Sun, 21 Jun 2020 18:19:17: 8000000 INFO @ Sun, 21 Jun 2020 18:19:21: 3000000 INFO @ Sun, 21 Jun 2020 18:19:22: 9000000 INFO @ Sun, 21 Jun 2020 18:19:27: 4000000 INFO @ Sun, 21 Jun 2020 18:19:28: 10000000 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 18:19:33: 5000000 INFO @ Sun, 21 Jun 2020 18:19:34: 11000000 INFO @ Sun, 21 Jun 2020 18:19:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.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 18:19:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:19:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:19:39: 6000000 INFO @ Sun, 21 Jun 2020 18:19:40: 1000000 INFO @ Sun, 21 Jun 2020 18:19:40: 12000000 INFO @ Sun, 21 Jun 2020 18:19:45: 7000000 INFO @ Sun, 21 Jun 2020 18:19:46: 2000000 INFO @ Sun, 21 Jun 2020 18:19:46: 13000000 INFO @ Sun, 21 Jun 2020 18:19:51: 8000000 INFO @ Sun, 21 Jun 2020 18:19:52: 3000000 INFO @ Sun, 21 Jun 2020 18:19:52: 14000000 INFO @ Sun, 21 Jun 2020 18:19:58: 9000000 INFO @ Sun, 21 Jun 2020 18:19:58: 4000000 INFO @ Sun, 21 Jun 2020 18:19:58: 15000000 INFO @ Sun, 21 Jun 2020 18:20:04: 10000000 INFO @ Sun, 21 Jun 2020 18:20:05: 5000000 INFO @ Sun, 21 Jun 2020 18:20:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:20:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:20:05: #1 total tags in treatment: 15985210 INFO @ Sun, 21 Jun 2020 18:20:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:05: #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 18:20:05: #1 tags after filtering in treatment: 15985186 INFO @ Sun, 21 Jun 2020 18:20:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:07: #2 number of paired peaks: 4447 INFO @ Sun, 21 Jun 2020 18:20:07: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:07: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:07: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:07: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:07: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 18:20:07: #2 alternative fragment length(s) may be 2,58,598 bps INFO @ Sun, 21 Jun 2020 18:20:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.05_model.r WARNING @ Sun, 21 Jun 2020 18:20:07: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:20:07: #2 You may need to consider one of the other alternative d(s): 2,58,598 WARNING @ Sun, 21 Jun 2020 18:20:07: #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 18:20:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:10: 11000000 INFO @ Sun, 21 Jun 2020 18:20:11: 6000000 INFO @ Sun, 21 Jun 2020 18:20:16: 12000000 INFO @ Sun, 21 Jun 2020 18:20:17: 7000000 INFO @ Sun, 21 Jun 2020 18:20:22: 13000000 INFO @ Sun, 21 Jun 2020 18:20:23: 8000000 INFO @ Sun, 21 Jun 2020 18:20:28: 14000000 INFO @ Sun, 21 Jun 2020 18:20:29: 9000000 INFO @ Sun, 21 Jun 2020 18:20:35: 15000000 INFO @ Sun, 21 Jun 2020 18:20:35: 10000000 INFO @ Sun, 21 Jun 2020 18:20:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:20:41: 11000000 INFO @ Sun, 21 Jun 2020 18:20:41: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:20:41: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:20:41: #1 total tags in treatment: 15985210 INFO @ Sun, 21 Jun 2020 18:20:41: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:20:41: #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 18:20:42: #1 tags after filtering in treatment: 15985186 INFO @ Sun, 21 Jun 2020 18:20:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:20:42: #1 finished! INFO @ Sun, 21 Jun 2020 18:20:42: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:20:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:20:43: #2 number of paired peaks: 4447 INFO @ Sun, 21 Jun 2020 18:20:43: start model_add_line... INFO @ Sun, 21 Jun 2020 18:20:43: start X-correlation... INFO @ Sun, 21 Jun 2020 18:20:43: end of X-cor INFO @ Sun, 21 Jun 2020 18:20:43: #2 finished! INFO @ Sun, 21 Jun 2020 18:20:43: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 18:20:43: #2 alternative fragment length(s) may be 2,58,598 bps INFO @ Sun, 21 Jun 2020 18:20:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.10_model.r WARNING @ Sun, 21 Jun 2020 18:20:43: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:20:43: #2 You may need to consider one of the other alternative d(s): 2,58,598 WARNING @ Sun, 21 Jun 2020 18:20:43: #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 18:20:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:20:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:20:47: 12000000 INFO @ Sun, 21 Jun 2020 18:20:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:20:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:20:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.05_summits.bed INFO @ Sun, 21 Jun 2020 18:20:49: Done! BedGraph に変換しました。 BigWig に変換中... pass1 - making usageList (1238 chroms): 2 millis pass2 - checking and writing primary data (6850 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:20:53: 13000000 INFO @ Sun, 21 Jun 2020 18:20:58: 14000000 INFO @ Sun, 21 Jun 2020 18:21:04: 15000000 INFO @ Sun, 21 Jun 2020 18:21:09: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:21:09: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:21:09: #1 total tags in treatment: 15985210 INFO @ Sun, 21 Jun 2020 18:21:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:21:09: #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 18:21:10: #1 tags after filtering in treatment: 15985186 INFO @ Sun, 21 Jun 2020 18:21:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:21:10: #1 finished! INFO @ Sun, 21 Jun 2020 18:21:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:21:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:21:11: #2 number of paired peaks: 4447 INFO @ Sun, 21 Jun 2020 18:21:11: start model_add_line... INFO @ Sun, 21 Jun 2020 18:21:11: start X-correlation... INFO @ Sun, 21 Jun 2020 18:21:11: end of X-cor INFO @ Sun, 21 Jun 2020 18:21:11: #2 finished! INFO @ Sun, 21 Jun 2020 18:21:11: #2 predicted fragment length is 58 bps INFO @ Sun, 21 Jun 2020 18:21:11: #2 alternative fragment length(s) may be 2,58,598 bps INFO @ Sun, 21 Jun 2020 18:21:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.20_model.r WARNING @ Sun, 21 Jun 2020 18:21:11: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:21:11: #2 You may need to consider one of the other alternative d(s): 2,58,598 WARNING @ Sun, 21 Jun 2020 18:21:11: #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 18:21:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:21:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:21:13: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:21:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.10_summits.bed INFO @ Sun, 21 Jun 2020 18:21:28: Done! pass1 - making usageList (930 chroms): 1 millis pass2 - checking and writing primary data (3402 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:21:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:21:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:21:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:21:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837288/SRX1837288.20_summits.bed INFO @ Sun, 21 Jun 2020 18:21:55: Done! pass1 - making usageList (647 chroms): 1 millis pass2 - checking and writing primary data (2192 records, 4 fields): 19 millis CompletedMACS2peakCalling