Job ID = 6455875 SRX = SRX3020541 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:19:07 prefetch.2.10.7: 1) Downloading 'SRR5850424'... 2020-06-21T10:19:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:19:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:19:46 prefetch.2.10.7: 'SRR5850424' is valid 2020-06-21T10:19:46 prefetch.2.10.7: 1) 'SRR5850424' was downloaded successfully 2020-06-21T10:19:46 prefetch.2.10.7: 'SRR5850424' has 0 unresolved dependencies Read 5159732 spots for SRR5850424/SRR5850424.sra Written 5159732 spots for SRR5850424/SRR5850424.sra 2020-06-21T10:20:15 prefetch.2.10.7: 1) Downloading 'SRR5850425'... 2020-06-21T10:20:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:19 prefetch.2.10.7: 'SRR5850425' is valid 2020-06-21T10:21:19 prefetch.2.10.7: 1) 'SRR5850425' was downloaded successfully 2020-06-21T10:21:19 prefetch.2.10.7: 'SRR5850425' has 0 unresolved dependencies Read 5110408 spots for SRR5850425/SRR5850425.sra Written 5110408 spots for SRR5850425/SRR5850425.sra 2020-06-21T10:21:48 prefetch.2.10.7: 1) Downloading 'SRR5850426'... 2020-06-21T10:21:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:34 prefetch.2.10.7: 'SRR5850426' is valid 2020-06-21T10:22:34 prefetch.2.10.7: 1) 'SRR5850426' was downloaded successfully 2020-06-21T10:22:34 prefetch.2.10.7: 'SRR5850426' has 0 unresolved dependencies Read 5105383 spots for SRR5850426/SRR5850426.sra Written 5105383 spots for SRR5850426/SRR5850426.sra 2020-06-21T10:23:06 prefetch.2.10.7: 1) Downloading 'SRR5850427'... 2020-06-21T10:23:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:47 prefetch.2.10.7: 'SRR5850427' is valid 2020-06-21T10:23:47 prefetch.2.10.7: 1) 'SRR5850427' was downloaded successfully 2020-06-21T10:23:47 prefetch.2.10.7: 'SRR5850427' has 0 unresolved dependencies Read 5064391 spots for SRR5850427/SRR5850427.sra Written 5064391 spots for SRR5850427/SRR5850427.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: 00:05:28 20439914 reads; of these: 20439914 (100.00%) were unpaired; of these: 684619 (3.35%) aligned 0 times 15005289 (73.41%) aligned exactly 1 time 4750006 (23.24%) aligned >1 times 96.65% overall alignment rate Time searching: 00:05:28 Overall time: 00:05:28 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] 3025570 / 19755295 = 0.1532 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 19:34:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.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 19:34:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:34:18: 1000000 INFO @ Sun, 21 Jun 2020 19:34:24: 2000000 INFO @ Sun, 21 Jun 2020 19:34:29: 3000000 INFO @ Sun, 21 Jun 2020 19:34:34: 4000000 INFO @ Sun, 21 Jun 2020 19:34:39: 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 19:34:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.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 19:34:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:34:44: 6000000 INFO @ Sun, 21 Jun 2020 19:34:49: 1000000 INFO @ Sun, 21 Jun 2020 19:34:50: 7000000 INFO @ Sun, 21 Jun 2020 19:34:54: 2000000 INFO @ Sun, 21 Jun 2020 19:34:55: 8000000 INFO @ Sun, 21 Jun 2020 19:35:00: 3000000 INFO @ Sun, 21 Jun 2020 19:35:00: 9000000 INFO @ Sun, 21 Jun 2020 19:35:05: 4000000 INFO @ Sun, 21 Jun 2020 19:35:06: 10000000 INFO @ Sun, 21 Jun 2020 19:35:10: 5000000 INFO @ Sun, 21 Jun 2020 19:35:11: 11000000 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 19:35:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.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 19:35:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:16: 6000000 INFO @ Sun, 21 Jun 2020 19:35:17: 12000000 INFO @ Sun, 21 Jun 2020 19:35:19: 1000000 INFO @ Sun, 21 Jun 2020 19:35:22: 7000000 INFO @ Sun, 21 Jun 2020 19:35:22: 13000000 INFO @ Sun, 21 Jun 2020 19:35:25: 2000000 INFO @ Sun, 21 Jun 2020 19:35:27: 8000000 INFO @ Sun, 21 Jun 2020 19:35:28: 14000000 INFO @ Sun, 21 Jun 2020 19:35:30: 3000000 INFO @ Sun, 21 Jun 2020 19:35:33: 9000000 INFO @ Sun, 21 Jun 2020 19:35:33: 15000000 INFO @ Sun, 21 Jun 2020 19:35:36: 4000000 INFO @ Sun, 21 Jun 2020 19:35:38: 10000000 INFO @ Sun, 21 Jun 2020 19:35:39: 16000000 INFO @ Sun, 21 Jun 2020 19:35:42: 5000000 INFO @ Sun, 21 Jun 2020 19:35:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:35:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:35:43: #1 total tags in treatment: 16729725 INFO @ Sun, 21 Jun 2020 19:35:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:35:43: #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 19:35:44: #1 tags after filtering in treatment: 16729621 INFO @ Sun, 21 Jun 2020 19:35:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:35:44: #1 finished! INFO @ Sun, 21 Jun 2020 19:35:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:35:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:35:44: 11000000 INFO @ Sun, 21 Jun 2020 19:35:45: #2 number of paired peaks: 1370 INFO @ Sun, 21 Jun 2020 19:35:45: start model_add_line... INFO @ Sun, 21 Jun 2020 19:35:45: start X-correlation... INFO @ Sun, 21 Jun 2020 19:35:45: end of X-cor INFO @ Sun, 21 Jun 2020 19:35:45: #2 finished! INFO @ Sun, 21 Jun 2020 19:35:45: #2 predicted fragment length is 86 bps INFO @ Sun, 21 Jun 2020 19:35:45: #2 alternative fragment length(s) may be 2,86 bps INFO @ Sun, 21 Jun 2020 19:35:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.05_model.r WARNING @ Sun, 21 Jun 2020 19:35:45: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:35:45: #2 You may need to consider one of the other alternative d(s): 2,86 WARNING @ Sun, 21 Jun 2020 19:35:45: #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 19:35:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:35:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:35:47: 6000000 INFO @ Sun, 21 Jun 2020 19:35:49: 12000000 INFO @ Sun, 21 Jun 2020 19:35:52: 7000000 INFO @ Sun, 21 Jun 2020 19:35:54: 13000000 INFO @ Sun, 21 Jun 2020 19:35:58: 8000000 INFO @ Sun, 21 Jun 2020 19:36:00: 14000000 INFO @ Sun, 21 Jun 2020 19:36:03: 9000000 INFO @ Sun, 21 Jun 2020 19:36:05: 15000000 INFO @ Sun, 21 Jun 2020 19:36:08: 10000000 INFO @ Sun, 21 Jun 2020 19:36:11: 16000000 INFO @ Sun, 21 Jun 2020 19:36:13: 11000000 INFO @ Sun, 21 Jun 2020 19:36:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:36:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:36:15: #1 total tags in treatment: 16729725 INFO @ Sun, 21 Jun 2020 19:36:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:15: #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 19:36:15: #1 tags after filtering in treatment: 16729621 INFO @ Sun, 21 Jun 2020 19:36:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:15: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:17: #2 number of paired peaks: 1370 INFO @ Sun, 21 Jun 2020 19:36:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:17: #2 predicted fragment length is 86 bps INFO @ Sun, 21 Jun 2020 19:36:17: #2 alternative fragment length(s) may be 2,86 bps INFO @ Sun, 21 Jun 2020 19:36:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.10_model.r WARNING @ Sun, 21 Jun 2020 19:36:17: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:36:17: #2 You may need to consider one of the other alternative d(s): 2,86 WARNING @ Sun, 21 Jun 2020 19:36:17: #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 19:36:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:19: 12000000 INFO @ Sun, 21 Jun 2020 19:36:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:24: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:36:29: 14000000 INFO @ Sun, 21 Jun 2020 19:36:34: 15000000 INFO @ Sun, 21 Jun 2020 19:36:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.05_summits.bed INFO @ Sun, 21 Jun 2020 19:36:39: Done! pass1 - making usageList (476 chroms): 1 millis pass2 - checking and writing primary data (3996 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:36:39: 16000000 INFO @ Sun, 21 Jun 2020 19:36:43: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:36:43: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:36:43: #1 total tags in treatment: 16729725 INFO @ Sun, 21 Jun 2020 19:36:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:43: #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 19:36:44: #1 tags after filtering in treatment: 16729621 INFO @ Sun, 21 Jun 2020 19:36:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:44: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:45: #2 number of paired peaks: 1370 INFO @ Sun, 21 Jun 2020 19:36:45: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:45: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:45: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:45: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:45: #2 predicted fragment length is 86 bps INFO @ Sun, 21 Jun 2020 19:36:45: #2 alternative fragment length(s) may be 2,86 bps INFO @ Sun, 21 Jun 2020 19:36:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.20_model.r WARNING @ Sun, 21 Jun 2020 19:36:45: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:36:45: #2 You may need to consider one of the other alternative d(s): 2,86 WARNING @ Sun, 21 Jun 2020 19:36:45: #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 19:36:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:54: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:37:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.10_summits.bed INFO @ Sun, 21 Jun 2020 19:37:13: Done! pass1 - making usageList (319 chroms): 1 millis pass2 - checking and writing primary data (1254 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:37:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020541/SRX3020541.20_summits.bed INFO @ Sun, 21 Jun 2020 19:37:40: Done! pass1 - making usageList (163 chroms): 1 millis pass2 - checking and writing primary data (434 records, 4 fields): 6 millis CompletedMACS2peakCalling