Job ID = 6453757 SRX = SRX1433400 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:29:56 prefetch.2.10.7: 1) Downloading 'SRR2919816'... 2020-06-21T08:29:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:35:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:35:05 prefetch.2.10.7: 1) 'SRR2919816' was downloaded successfully Read 56185355 spots for SRR2919816/SRR2919816.sra Written 56185355 spots for SRR2919816/SRR2919816.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:24 56185355 reads; of these: 56185355 (100.00%) were unpaired; of these: 6149908 (10.95%) aligned 0 times 36050588 (64.16%) aligned exactly 1 time 13984859 (24.89%) aligned >1 times 89.05% overall alignment rate Time searching: 00:12:25 Overall time: 00:12:25 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 24 files... [bam_rmdupse_core] 29735256 / 50035447 = 0.5943 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 17:57:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.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 17:57:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:57:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:57:13: 1000000 INFO @ Sun, 21 Jun 2020 17:57:18: 2000000 INFO @ Sun, 21 Jun 2020 17:57:23: 3000000 INFO @ Sun, 21 Jun 2020 17:57:28: 4000000 INFO @ Sun, 21 Jun 2020 17:57:33: 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 17:57:37: 6000000 INFO @ Sun, 21 Jun 2020 17:57:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.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 17:57:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:57:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:57:42: 7000000 INFO @ Sun, 21 Jun 2020 17:57:43: 1000000 INFO @ Sun, 21 Jun 2020 17:57:48: 8000000 INFO @ Sun, 21 Jun 2020 17:57:48: 2000000 INFO @ Sun, 21 Jun 2020 17:57:53: 9000000 INFO @ Sun, 21 Jun 2020 17:57:54: 3000000 INFO @ Sun, 21 Jun 2020 17:57:58: 10000000 INFO @ Sun, 21 Jun 2020 17:57:59: 4000000 INFO @ Sun, 21 Jun 2020 17:58:03: 11000000 INFO @ Sun, 21 Jun 2020 17:58:04: 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 17:58:08: 12000000 INFO @ Sun, 21 Jun 2020 17:58:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.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 17:58:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:58:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:58:09: 6000000 INFO @ Sun, 21 Jun 2020 17:58:13: 13000000 INFO @ Sun, 21 Jun 2020 17:58:14: 7000000 INFO @ Sun, 21 Jun 2020 17:58:14: 1000000 INFO @ Sun, 21 Jun 2020 17:58:18: 14000000 INFO @ Sun, 21 Jun 2020 17:58:19: 8000000 INFO @ Sun, 21 Jun 2020 17:58:19: 2000000 INFO @ Sun, 21 Jun 2020 17:58:23: 15000000 INFO @ Sun, 21 Jun 2020 17:58:24: 9000000 INFO @ Sun, 21 Jun 2020 17:58:24: 3000000 INFO @ Sun, 21 Jun 2020 17:58:28: 16000000 INFO @ Sun, 21 Jun 2020 17:58:30: 10000000 INFO @ Sun, 21 Jun 2020 17:58:30: 4000000 INFO @ Sun, 21 Jun 2020 17:58:34: 17000000 INFO @ Sun, 21 Jun 2020 17:58:35: 11000000 INFO @ Sun, 21 Jun 2020 17:58:35: 5000000 INFO @ Sun, 21 Jun 2020 17:58:39: 18000000 INFO @ Sun, 21 Jun 2020 17:58:40: 6000000 INFO @ Sun, 21 Jun 2020 17:58:40: 12000000 INFO @ Sun, 21 Jun 2020 17:58:44: 19000000 INFO @ Sun, 21 Jun 2020 17:58:45: 7000000 INFO @ Sun, 21 Jun 2020 17:58:45: 13000000 INFO @ Sun, 21 Jun 2020 17:58:50: 20000000 INFO @ Sun, 21 Jun 2020 17:58:50: 8000000 INFO @ Sun, 21 Jun 2020 17:58:50: 14000000 INFO @ Sun, 21 Jun 2020 17:58:51: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 17:58:51: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 17:58:51: #1 total tags in treatment: 20300191 INFO @ Sun, 21 Jun 2020 17:58:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:58:51: #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 17:58:52: #1 tags after filtering in treatment: 20300128 INFO @ Sun, 21 Jun 2020 17:58:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:58:52: #1 finished! INFO @ Sun, 21 Jun 2020 17:58:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:58:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:58:53: #2 number of paired peaks: 1243 INFO @ Sun, 21 Jun 2020 17:58:53: start model_add_line... INFO @ Sun, 21 Jun 2020 17:58:54: start X-correlation... INFO @ Sun, 21 Jun 2020 17:58:54: end of X-cor INFO @ Sun, 21 Jun 2020 17:58:54: #2 finished! INFO @ Sun, 21 Jun 2020 17:58:54: #2 predicted fragment length is 121 bps INFO @ Sun, 21 Jun 2020 17:58:54: #2 alternative fragment length(s) may be 2,121 bps INFO @ Sun, 21 Jun 2020 17:58:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.05_model.r INFO @ Sun, 21 Jun 2020 17:58:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:58:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:58:55: 9000000 INFO @ Sun, 21 Jun 2020 17:58:56: 15000000 INFO @ Sun, 21 Jun 2020 17:59:00: 10000000 INFO @ Sun, 21 Jun 2020 17:59:01: 16000000 INFO @ Sun, 21 Jun 2020 17:59:05: 11000000 INFO @ Sun, 21 Jun 2020 17:59:06: 17000000 INFO @ Sun, 21 Jun 2020 17:59:11: 12000000 INFO @ Sun, 21 Jun 2020 17:59:12: 18000000 INFO @ Sun, 21 Jun 2020 17:59:16: 13000000 INFO @ Sun, 21 Jun 2020 17:59:17: 19000000 INFO @ Sun, 21 Jun 2020 17:59:21: 14000000 INFO @ Sun, 21 Jun 2020 17:59:23: 20000000 INFO @ Sun, 21 Jun 2020 17:59:24: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 17:59:24: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 17:59:24: #1 total tags in treatment: 20300191 INFO @ Sun, 21 Jun 2020 17:59:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:59:24: #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 17:59:25: #1 tags after filtering in treatment: 20300128 INFO @ Sun, 21 Jun 2020 17:59:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:59:25: #1 finished! INFO @ Sun, 21 Jun 2020 17:59:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:59:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:59:26: 15000000 INFO @ Sun, 21 Jun 2020 17:59:26: #2 number of paired peaks: 1243 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 121 bps INFO @ Sun, 21 Jun 2020 17:59:26: #2 alternative fragment length(s) may be 2,121 bps INFO @ Sun, 21 Jun 2020 17:59:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.10_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 17:59:31: 16000000 INFO @ Sun, 21 Jun 2020 17:59:34: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:59:36: 17000000 INFO @ Sun, 21 Jun 2020 17:59:41: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:59:46: 19000000 INFO @ Sun, 21 Jun 2020 17:59:51: 20000000 INFO @ Sun, 21 Jun 2020 17:59:53: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 17:59:53: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 17:59:53: #1 total tags in treatment: 20300191 INFO @ Sun, 21 Jun 2020 17:59:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:59:53: #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 17:59:53: #1 tags after filtering in treatment: 20300128 INFO @ Sun, 21 Jun 2020 17:59:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:59:53: #1 finished! INFO @ Sun, 21 Jun 2020 17:59:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:59:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:59:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:59:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:59:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.05_summits.bed INFO @ Sun, 21 Jun 2020 17:59:55: #2 number of paired peaks: 1243 INFO @ Sun, 21 Jun 2020 17:59:55: start model_add_line... INFO @ Sun, 21 Jun 2020 17:59:55: Done! INFO @ Sun, 21 Jun 2020 17:59:55: start X-correlation... INFO @ Sun, 21 Jun 2020 17:59:55: end of X-cor INFO @ Sun, 21 Jun 2020 17:59:55: #2 finished! INFO @ Sun, 21 Jun 2020 17:59:55: #2 predicted fragment length is 121 bps INFO @ Sun, 21 Jun 2020 17:59:55: #2 alternative fragment length(s) may be 2,121 bps INFO @ Sun, 21 Jun 2020 17:59:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.20_model.r INFO @ Sun, 21 Jun 2020 17:59:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:59:55: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (730 chroms): 2 millis pass2 - checking and writing primary data (4713 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:00:08: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:00:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:00:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:00:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.10_summits.bed INFO @ Sun, 21 Jun 2020 18:00:28: Done! pass1 - making usageList (598 chroms): 1 millis pass2 - checking and writing primary data (2876 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:00:37: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:00:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:00:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:00:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433400/SRX1433400.20_summits.bed INFO @ Sun, 21 Jun 2020 18:00:57: Done! pass1 - making usageList (453 chroms): 2 millis pass2 - checking and writing primary data (1437 records, 4 fields): 13 millis CompletedMACS2peakCalling