Job ID = 6455870 SRX = SRX3020536 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:24:51 prefetch.2.10.7: 1) Downloading 'SRR5850404'... 2020-06-21T10:24:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:25:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:25:43 prefetch.2.10.7: 'SRR5850404' is valid 2020-06-21T10:25:43 prefetch.2.10.7: 1) 'SRR5850404' was downloaded successfully 2020-06-21T10:25:43 prefetch.2.10.7: 'SRR5850404' has 0 unresolved dependencies Read 7468333 spots for SRR5850404/SRR5850404.sra Written 7468333 spots for SRR5850404/SRR5850404.sra 2020-06-21T10:26:20 prefetch.2.10.7: 1) Downloading 'SRR5850405'... 2020-06-21T10:26:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:27:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:27:14 prefetch.2.10.7: 'SRR5850405' is valid 2020-06-21T10:27:14 prefetch.2.10.7: 1) 'SRR5850405' was downloaded successfully 2020-06-21T10:27:14 prefetch.2.10.7: 'SRR5850405' has 0 unresolved dependencies Read 7458215 spots for SRR5850405/SRR5850405.sra Written 7458215 spots for SRR5850405/SRR5850405.sra 2020-06-21T10:27:51 prefetch.2.10.7: 1) Downloading 'SRR5850406'... 2020-06-21T10:27:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:28:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:28:37 prefetch.2.10.7: 'SRR5850406' is valid 2020-06-21T10:28:37 prefetch.2.10.7: 1) 'SRR5850406' was downloaded successfully 2020-06-21T10:28:37 prefetch.2.10.7: 'SRR5850406' has 0 unresolved dependencies Read 7462041 spots for SRR5850406/SRR5850406.sra Written 7462041 spots for SRR5850406/SRR5850406.sra 2020-06-21T10:29:14 prefetch.2.10.7: 1) Downloading 'SRR5850407'... 2020-06-21T10:29:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:30:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:30:07 prefetch.2.10.7: 'SRR5850407' is valid 2020-06-21T10:30:07 prefetch.2.10.7: 1) 'SRR5850407' was downloaded successfully 2020-06-21T10:30:07 prefetch.2.10.7: 'SRR5850407' has 0 unresolved dependencies Read 7416886 spots for SRR5850407/SRR5850407.sra Written 7416886 spots for SRR5850407/SRR5850407.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: 00:07:22 29805475 reads; of these: 29805475 (100.00%) were unpaired; of these: 4947497 (16.60%) aligned 0 times 19052122 (63.92%) aligned exactly 1 time 5805856 (19.48%) aligned >1 times 83.40% overall alignment rate Time searching: 00:07:22 Overall time: 00:07:22 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] 5449511 / 24857978 = 0.2192 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 19:43:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.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 19:43:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:43:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:43:27: 1000000 INFO @ Sun, 21 Jun 2020 19:43:32: 2000000 INFO @ Sun, 21 Jun 2020 19:43:37: 3000000 INFO @ Sun, 21 Jun 2020 19:43:42: 4000000 INFO @ Sun, 21 Jun 2020 19:43:47: 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 19:43:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.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 19:43:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:43:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:43:52: 6000000 INFO @ Sun, 21 Jun 2020 19:43:57: 7000000 INFO @ Sun, 21 Jun 2020 19:43:57: 1000000 INFO @ Sun, 21 Jun 2020 19:44:02: 8000000 INFO @ Sun, 21 Jun 2020 19:44:02: 2000000 INFO @ Sun, 21 Jun 2020 19:44:07: 9000000 INFO @ Sun, 21 Jun 2020 19:44:07: 3000000 INFO @ Sun, 21 Jun 2020 19:44:13: 10000000 INFO @ Sun, 21 Jun 2020 19:44:13: 4000000 INFO @ Sun, 21 Jun 2020 19:44:18: 11000000 INFO @ Sun, 21 Jun 2020 19:44:18: 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 19:44:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.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 19:44:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:44:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:44:23: 6000000 INFO @ Sun, 21 Jun 2020 19:44:23: 12000000 INFO @ Sun, 21 Jun 2020 19:44:28: 1000000 INFO @ Sun, 21 Jun 2020 19:44:29: 7000000 INFO @ Sun, 21 Jun 2020 19:44:29: 13000000 INFO @ Sun, 21 Jun 2020 19:44:34: 2000000 INFO @ Sun, 21 Jun 2020 19:44:35: 8000000 INFO @ Sun, 21 Jun 2020 19:44:35: 14000000 INFO @ Sun, 21 Jun 2020 19:44:40: 3000000 INFO @ Sun, 21 Jun 2020 19:44:40: 9000000 INFO @ Sun, 21 Jun 2020 19:44:40: 15000000 INFO @ Sun, 21 Jun 2020 19:44:46: 10000000 INFO @ Sun, 21 Jun 2020 19:44:46: 4000000 INFO @ Sun, 21 Jun 2020 19:44:46: 16000000 INFO @ Sun, 21 Jun 2020 19:44:51: 11000000 INFO @ Sun, 21 Jun 2020 19:44:52: 5000000 INFO @ Sun, 21 Jun 2020 19:44:52: 17000000 INFO @ Sun, 21 Jun 2020 19:44:57: 12000000 INFO @ Sun, 21 Jun 2020 19:44:58: 18000000 INFO @ Sun, 21 Jun 2020 19:44:58: 6000000 INFO @ Sun, 21 Jun 2020 19:45:03: 13000000 INFO @ Sun, 21 Jun 2020 19:45:03: 19000000 INFO @ Sun, 21 Jun 2020 19:45:04: 7000000 INFO @ Sun, 21 Jun 2020 19:45:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:45:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:45:06: #1 total tags in treatment: 19408467 INFO @ Sun, 21 Jun 2020 19:45:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:45:06: #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 19:45:07: #1 tags after filtering in treatment: 19408379 INFO @ Sun, 21 Jun 2020 19:45:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:45:07: #1 finished! INFO @ Sun, 21 Jun 2020 19:45:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:45:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:45:08: #2 number of paired peaks: 4005 INFO @ Sun, 21 Jun 2020 19:45:08: start model_add_line... INFO @ Sun, 21 Jun 2020 19:45:08: 14000000 INFO @ Sun, 21 Jun 2020 19:45:09: start X-correlation... INFO @ Sun, 21 Jun 2020 19:45:09: end of X-cor INFO @ Sun, 21 Jun 2020 19:45:09: #2 finished! INFO @ Sun, 21 Jun 2020 19:45:09: #2 predicted fragment length is 131 bps INFO @ Sun, 21 Jun 2020 19:45:09: #2 alternative fragment length(s) may be 2,131 bps INFO @ Sun, 21 Jun 2020 19:45:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.05_model.r INFO @ Sun, 21 Jun 2020 19:45:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:45:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:45:10: 8000000 INFO @ Sun, 21 Jun 2020 19:45:14: 15000000 INFO @ Sun, 21 Jun 2020 19:45:16: 9000000 INFO @ Sun, 21 Jun 2020 19:45:20: 16000000 INFO @ Sun, 21 Jun 2020 19:45:22: 10000000 INFO @ Sun, 21 Jun 2020 19:45:26: 17000000 INFO @ Sun, 21 Jun 2020 19:45:28: 11000000 INFO @ Sun, 21 Jun 2020 19:45:31: 18000000 INFO @ Sun, 21 Jun 2020 19:45:34: 12000000 INFO @ Sun, 21 Jun 2020 19:45:37: 19000000 INFO @ Sun, 21 Jun 2020 19:45:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:45:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:45:40: #1 total tags in treatment: 19408467 INFO @ Sun, 21 Jun 2020 19:45:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:45:40: #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 19:45:41: 13000000 INFO @ Sun, 21 Jun 2020 19:45:41: #1 tags after filtering in treatment: 19408379 INFO @ Sun, 21 Jun 2020 19:45:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:45:41: #1 finished! INFO @ Sun, 21 Jun 2020 19:45:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:45:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:45:42: #2 number of paired peaks: 4005 INFO @ Sun, 21 Jun 2020 19:45:42: start model_add_line... INFO @ Sun, 21 Jun 2020 19:45:43: start X-correlation... INFO @ Sun, 21 Jun 2020 19:45:43: end of X-cor INFO @ Sun, 21 Jun 2020 19:45:43: #2 finished! INFO @ Sun, 21 Jun 2020 19:45:43: #2 predicted fragment length is 131 bps INFO @ Sun, 21 Jun 2020 19:45:43: #2 alternative fragment length(s) may be 2,131 bps INFO @ Sun, 21 Jun 2020 19:45:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.10_model.r INFO @ Sun, 21 Jun 2020 19:45:43: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:45:43: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:45:47: 14000000 INFO @ Sun, 21 Jun 2020 19:45:52: 15000000 INFO @ Sun, 21 Jun 2020 19:45:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:45:58: 16000000 INFO @ Sun, 21 Jun 2020 19:46:05: 17000000 INFO @ Sun, 21 Jun 2020 19:46:11: 18000000 INFO @ Sun, 21 Jun 2020 19:46:18: 19000000 INFO @ Sun, 21 Jun 2020 19:46:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:46:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:46:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.05_summits.bed INFO @ Sun, 21 Jun 2020 19:46:19: Done! pass1 - making usageList (503 chroms): 3 millis pass2 - checking and writing primary data (9489 records, 4 fields): 25 millis INFO @ Sun, 21 Jun 2020 19:46:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:46:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:46:20: #1 total tags in treatment: 19408467 INFO @ Sun, 21 Jun 2020 19:46:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:46:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:46:21: #1 tags after filtering in treatment: 19408379 INFO @ Sun, 21 Jun 2020 19:46:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:46:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:46:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:46:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:46:23: #2 number of paired peaks: 4005 INFO @ Sun, 21 Jun 2020 19:46:23: start model_add_line... INFO @ Sun, 21 Jun 2020 19:46:23: start X-correlation... INFO @ Sun, 21 Jun 2020 19:46:23: end of X-cor INFO @ Sun, 21 Jun 2020 19:46:23: #2 finished! INFO @ Sun, 21 Jun 2020 19:46:23: #2 predicted fragment length is 131 bps INFO @ Sun, 21 Jun 2020 19:46:23: #2 alternative fragment length(s) may be 2,131 bps INFO @ Sun, 21 Jun 2020 19:46:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.20_model.r INFO @ Sun, 21 Jun 2020 19:46:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:46:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:46:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:46:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:46:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:46:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.10_summits.bed INFO @ Sun, 21 Jun 2020 19:46:53: Done! pass1 - making usageList (353 chroms): 2 millis pass2 - checking and writing primary data (5027 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:47:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:47:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:47:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:47:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3020536/SRX3020536.20_summits.bed INFO @ Sun, 21 Jun 2020 19:47:34: Done! pass1 - making usageList (198 chroms): 1 millis pass2 - checking and writing primary data (1608 records, 4 fields): 9 millis CompletedMACS2peakCalling