Job ID = 6453579 SRX = SRX128169 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:29:41 prefetch.2.10.7: 1) Downloading 'SRR442090'... 2020-06-21T08:29:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:36:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:36:38 prefetch.2.10.7: 1) 'SRR442090' was downloaded successfully Read 36531342 spots for SRR442090/SRR442090.sra Written 36531342 spots for SRR442090/SRR442090.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: 00:08:00 36531342 reads; of these: 36531342 (100.00%) were unpaired; of these: 1761463 (4.82%) aligned 0 times 29182233 (79.88%) aligned exactly 1 time 5587646 (15.30%) aligned >1 times 95.18% overall alignment rate Time searching: 00:08:00 Overall time: 00:08:00 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] 12963544 / 34769879 = 0.3728 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 17:56:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.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 17:56:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:56:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:56:13: 1000000 INFO @ Sun, 21 Jun 2020 17:56:20: 2000000 INFO @ Sun, 21 Jun 2020 17:56:25: 3000000 INFO @ Sun, 21 Jun 2020 17:56:31: 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 17:56:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.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 17:56:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:56:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:56:37: 5000000 INFO @ Sun, 21 Jun 2020 17:56:43: 6000000 INFO @ Sun, 21 Jun 2020 17:56:43: 1000000 INFO @ Sun, 21 Jun 2020 17:56:49: 7000000 INFO @ Sun, 21 Jun 2020 17:56:49: 2000000 INFO @ Sun, 21 Jun 2020 17:56:56: 8000000 INFO @ Sun, 21 Jun 2020 17:56:56: 3000000 INFO @ Sun, 21 Jun 2020 17:57:02: 9000000 INFO @ Sun, 21 Jun 2020 17:57:02: 4000000 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 17:57:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.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 17:57:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:57:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:57:08: 5000000 INFO @ Sun, 21 Jun 2020 17:57:08: 10000000 INFO @ Sun, 21 Jun 2020 17:57:14: 1000000 INFO @ Sun, 21 Jun 2020 17:57:15: 6000000 INFO @ Sun, 21 Jun 2020 17:57:15: 11000000 INFO @ Sun, 21 Jun 2020 17:57:21: 2000000 INFO @ Sun, 21 Jun 2020 17:57:22: 12000000 INFO @ Sun, 21 Jun 2020 17:57:22: 7000000 INFO @ Sun, 21 Jun 2020 17:57:28: 3000000 INFO @ Sun, 21 Jun 2020 17:57:28: 13000000 INFO @ Sun, 21 Jun 2020 17:57:29: 8000000 INFO @ Sun, 21 Jun 2020 17:57:34: 14000000 INFO @ Sun, 21 Jun 2020 17:57:34: 4000000 INFO @ Sun, 21 Jun 2020 17:57:35: 9000000 INFO @ Sun, 21 Jun 2020 17:57:40: 15000000 INFO @ Sun, 21 Jun 2020 17:57:40: 5000000 INFO @ Sun, 21 Jun 2020 17:57:41: 10000000 INFO @ Sun, 21 Jun 2020 17:57:45: 16000000 INFO @ Sun, 21 Jun 2020 17:57:47: 6000000 INFO @ Sun, 21 Jun 2020 17:57:48: 11000000 INFO @ Sun, 21 Jun 2020 17:57:51: 17000000 INFO @ Sun, 21 Jun 2020 17:57:53: 7000000 INFO @ Sun, 21 Jun 2020 17:57:54: 12000000 INFO @ Sun, 21 Jun 2020 17:57:57: 18000000 INFO @ Sun, 21 Jun 2020 17:58:00: 8000000 INFO @ Sun, 21 Jun 2020 17:58:00: 13000000 INFO @ Sun, 21 Jun 2020 17:58:03: 19000000 INFO @ Sun, 21 Jun 2020 17:58:06: 9000000 INFO @ Sun, 21 Jun 2020 17:58:06: 14000000 INFO @ Sun, 21 Jun 2020 17:58:09: 20000000 INFO @ Sun, 21 Jun 2020 17:58:12: 15000000 INFO @ Sun, 21 Jun 2020 17:58:12: 10000000 INFO @ Sun, 21 Jun 2020 17:58:14: 21000000 INFO @ Sun, 21 Jun 2020 17:58:18: 16000000 INFO @ Sun, 21 Jun 2020 17:58:19: 11000000 INFO @ Sun, 21 Jun 2020 17:58:20: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:58:20: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:58:20: #1 total tags in treatment: 21806335 INFO @ Sun, 21 Jun 2020 17:58:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:58:20: #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 17:58:21: #1 tags after filtering in treatment: 21806243 INFO @ Sun, 21 Jun 2020 17:58:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:58:21: #1 finished! INFO @ Sun, 21 Jun 2020 17:58:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:58:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:58:22: #2 number of paired peaks: 2185 INFO @ Sun, 21 Jun 2020 17:58:22: start model_add_line... INFO @ Sun, 21 Jun 2020 17:58:23: start X-correlation... INFO @ Sun, 21 Jun 2020 17:58:23: end of X-cor INFO @ Sun, 21 Jun 2020 17:58:23: #2 finished! INFO @ Sun, 21 Jun 2020 17:58:23: #2 predicted fragment length is 160 bps INFO @ Sun, 21 Jun 2020 17:58:23: #2 alternative fragment length(s) may be 4,160 bps INFO @ Sun, 21 Jun 2020 17:58:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.05_model.r INFO @ Sun, 21 Jun 2020 17:58:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:58:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:58:24: 17000000 INFO @ Sun, 21 Jun 2020 17:58:25: 12000000 INFO @ Sun, 21 Jun 2020 17:58:31: 13000000 INFO @ Sun, 21 Jun 2020 17:58:32: 18000000 INFO @ Sun, 21 Jun 2020 17:58:37: 14000000 INFO @ Sun, 21 Jun 2020 17:58:38: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:58:43: 15000000 INFO @ Sun, 21 Jun 2020 17:58:44: 20000000 INFO @ Sun, 21 Jun 2020 17:58:49: 16000000 INFO @ Sun, 21 Jun 2020 17:58:50: 21000000 INFO @ Sun, 21 Jun 2020 17:58:55: 17000000 INFO @ Sun, 21 Jun 2020 17:58:56: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:58:56: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:58:56: #1 total tags in treatment: 21806335 INFO @ Sun, 21 Jun 2020 17:58:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:58:56: #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 17:58:57: #1 tags after filtering in treatment: 21806243 INFO @ Sun, 21 Jun 2020 17:58:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:58:57: #1 finished! INFO @ Sun, 21 Jun 2020 17:58:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:58:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:58:58: #2 number of paired peaks: 2185 INFO @ Sun, 21 Jun 2020 17:58:58: start model_add_line... INFO @ Sun, 21 Jun 2020 17:58:59: start X-correlation... INFO @ Sun, 21 Jun 2020 17:58:59: end of X-cor INFO @ Sun, 21 Jun 2020 17:58:59: #2 finished! INFO @ Sun, 21 Jun 2020 17:58:59: #2 predicted fragment length is 160 bps INFO @ Sun, 21 Jun 2020 17:58:59: #2 alternative fragment length(s) may be 4,160 bps INFO @ Sun, 21 Jun 2020 17:58:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.10_model.r INFO @ Sun, 21 Jun 2020 17:58:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:58:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:59:01: 18000000 INFO @ Sun, 21 Jun 2020 17:59:07: 19000000 INFO @ Sun, 21 Jun 2020 17:59:13: 20000000 INFO @ Sun, 21 Jun 2020 17:59:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:59:18: 21000000 INFO @ Sun, 21 Jun 2020 17:59:23: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:59:23: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:59:23: #1 total tags in treatment: 21806335 INFO @ Sun, 21 Jun 2020 17:59:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:59:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:59:24: #1 tags after filtering in treatment: 21806243 INFO @ Sun, 21 Jun 2020 17:59:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:59:24: #1 finished! INFO @ Sun, 21 Jun 2020 17:59:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:59:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:59:26: #2 number of paired peaks: 2185 INFO @ Sun, 21 Jun 2020 17:59:26: start model_add_line... INFO @ Sun, 21 Jun 2020 17:59:26: start X-correlation... INFO @ Sun, 21 Jun 2020 17:59:26: end of X-cor INFO @ Sun, 21 Jun 2020 17:59:26: #2 finished! INFO @ Sun, 21 Jun 2020 17:59:26: #2 predicted fragment length is 160 bps INFO @ Sun, 21 Jun 2020 17:59:26: #2 alternative fragment length(s) may be 4,160 bps INFO @ Sun, 21 Jun 2020 17:59:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.20_model.r INFO @ Sun, 21 Jun 2020 17:59:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:59:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:59:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:59:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:59:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.05_summits.bed INFO @ Sun, 21 Jun 2020 17:59:37: Done! pass1 - making usageList (159 chroms): 4 millis pass2 - checking and writing primary data (17453 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:59:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:00:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:00:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:00:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.10_summits.bed INFO @ Sun, 21 Jun 2020 18:00:15: Done! pass1 - making usageList (123 chroms): 3 millis pass2 - checking and writing primary data (11030 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:00:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:00:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:00:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:00:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX128169/SRX128169.20_summits.bed INFO @ Sun, 21 Jun 2020 18:00:40: Done! pass1 - making usageList (94 chroms): 1 millis pass2 - checking and writing primary data (4416 records, 4 fields): 12 millis CompletedMACS2peakCalling