Job ID = 6455660 SRX = SRX287965 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:05:40 prefetch.2.10.7: 1) Downloading 'SRR870154'... 2020-06-21T10:05:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:10:35 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:10:36 prefetch.2.10.7: 'SRR870154' is valid 2020-06-21T10:10:36 prefetch.2.10.7: 1) 'SRR870154' was downloaded successfully Read 15295346 spots for SRR870154/SRR870154.sra Written 15295346 spots for SRR870154/SRR870154.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: 00:03:18 15295346 reads; of these: 15295346 (100.00%) were unpaired; of these: 1226376 (8.02%) aligned 0 times 13055106 (85.35%) aligned exactly 1 time 1013864 (6.63%) aligned >1 times 91.98% overall alignment rate Time searching: 00:03:18 Overall time: 00:03:18 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 8 files... [bam_rmdupse_core] 1562579 / 14068970 = 0.1111 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 19:18:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.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 19:18:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:18:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:18:38: 1000000 INFO @ Sun, 21 Jun 2020 19:18:44: 2000000 INFO @ Sun, 21 Jun 2020 19:18:50: 3000000 INFO @ Sun, 21 Jun 2020 19:18:56: 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 19:19:02: 5000000 INFO @ Sun, 21 Jun 2020 19:19:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.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 19:19:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:19:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:19:09: 6000000 INFO @ Sun, 21 Jun 2020 19:19:10: 1000000 INFO @ Sun, 21 Jun 2020 19:19:15: 7000000 INFO @ Sun, 21 Jun 2020 19:19:17: 2000000 INFO @ Sun, 21 Jun 2020 19:19:22: 8000000 INFO @ Sun, 21 Jun 2020 19:19:23: 3000000 INFO @ Sun, 21 Jun 2020 19:19:29: 9000000 INFO @ Sun, 21 Jun 2020 19:19:30: 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 19:19:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.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 19:19:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:19:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:19:36: 10000000 INFO @ Sun, 21 Jun 2020 19:19:37: 5000000 INFO @ Sun, 21 Jun 2020 19:19:39: 1000000 INFO @ Sun, 21 Jun 2020 19:19:43: 11000000 INFO @ Sun, 21 Jun 2020 19:19:44: 6000000 INFO @ Sun, 21 Jun 2020 19:19:46: 2000000 INFO @ Sun, 21 Jun 2020 19:19:49: 12000000 INFO @ Sun, 21 Jun 2020 19:19:50: 7000000 INFO @ Sun, 21 Jun 2020 19:19:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:19:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:19:53: #1 total tags in treatment: 12506391 INFO @ Sun, 21 Jun 2020 19:19:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:19:53: #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 19:19:53: 3000000 INFO @ Sun, 21 Jun 2020 19:19:53: #1 tags after filtering in treatment: 12506334 INFO @ Sun, 21 Jun 2020 19:19:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:19:53: #1 finished! INFO @ Sun, 21 Jun 2020 19:19:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:19:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:19:54: #2 number of paired peaks: 2272 INFO @ Sun, 21 Jun 2020 19:19:54: start model_add_line... INFO @ Sun, 21 Jun 2020 19:19:55: start X-correlation... INFO @ Sun, 21 Jun 2020 19:19:55: end of X-cor INFO @ Sun, 21 Jun 2020 19:19:55: #2 finished! INFO @ Sun, 21 Jun 2020 19:19:55: #2 predicted fragment length is 201 bps INFO @ Sun, 21 Jun 2020 19:19:55: #2 alternative fragment length(s) may be 201 bps INFO @ Sun, 21 Jun 2020 19:19:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.05_model.r INFO @ Sun, 21 Jun 2020 19:19:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:19:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:19:57: 8000000 INFO @ Sun, 21 Jun 2020 19:20:00: 4000000 INFO @ Sun, 21 Jun 2020 19:20:04: 9000000 INFO @ Sun, 21 Jun 2020 19:20:07: 5000000 INFO @ Sun, 21 Jun 2020 19:20:10: 10000000 INFO @ Sun, 21 Jun 2020 19:20:13: 6000000 INFO @ Sun, 21 Jun 2020 19:20:17: 11000000 INFO @ Sun, 21 Jun 2020 19:20:20: 7000000 INFO @ Sun, 21 Jun 2020 19:20:24: 12000000 INFO @ Sun, 21 Jun 2020 19:20:26: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:20:27: 8000000 INFO @ Sun, 21 Jun 2020 19:20:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:20:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:20:28: #1 total tags in treatment: 12506391 INFO @ Sun, 21 Jun 2020 19:20:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:20:28: #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 19:20:28: #1 tags after filtering in treatment: 12506334 INFO @ Sun, 21 Jun 2020 19:20:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:20:28: #1 finished! INFO @ Sun, 21 Jun 2020 19:20:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:20:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:20:29: #2 number of paired peaks: 2272 INFO @ Sun, 21 Jun 2020 19:20:29: start model_add_line... INFO @ Sun, 21 Jun 2020 19:20:29: start X-correlation... INFO @ Sun, 21 Jun 2020 19:20:29: end of X-cor INFO @ Sun, 21 Jun 2020 19:20:29: #2 finished! INFO @ Sun, 21 Jun 2020 19:20:29: #2 predicted fragment length is 201 bps INFO @ Sun, 21 Jun 2020 19:20:29: #2 alternative fragment length(s) may be 201 bps INFO @ Sun, 21 Jun 2020 19:20:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.10_model.r INFO @ Sun, 21 Jun 2020 19:20:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:20:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:20:33: 9000000 INFO @ Sun, 21 Jun 2020 19:20:39: 10000000 INFO @ Sun, 21 Jun 2020 19:20:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:20:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:20:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.05_summits.bed INFO @ Sun, 21 Jun 2020 19:20:42: Done! pass1 - making usageList (86 chroms): 2 millis pass2 - checking and writing primary data (7788 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:20:46: 11000000 INFO @ Sun, 21 Jun 2020 19:20:52: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:20:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:20:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:20:55: #1 total tags in treatment: 12506391 INFO @ Sun, 21 Jun 2020 19:20:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:20:55: #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 19:20:56: #1 tags after filtering in treatment: 12506334 INFO @ Sun, 21 Jun 2020 19:20:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:20:56: #1 finished! INFO @ Sun, 21 Jun 2020 19:20:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:20:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:20:57: #2 number of paired peaks: 2272 INFO @ Sun, 21 Jun 2020 19:20:57: start model_add_line... INFO @ Sun, 21 Jun 2020 19:20:57: start X-correlation... INFO @ Sun, 21 Jun 2020 19:20:57: end of X-cor INFO @ Sun, 21 Jun 2020 19:20:57: #2 finished! INFO @ Sun, 21 Jun 2020 19:20:57: #2 predicted fragment length is 201 bps INFO @ Sun, 21 Jun 2020 19:20:57: #2 alternative fragment length(s) may be 201 bps INFO @ Sun, 21 Jun 2020 19:20:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.20_model.r INFO @ Sun, 21 Jun 2020 19:20:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:20:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:21:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:21:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:21:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:21:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.10_summits.bed INFO @ Sun, 21 Jun 2020 19:21:18: Done! pass1 - making usageList (67 chroms): 1 millis pass2 - checking and writing primary data (4546 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:21:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:21:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:21:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:21:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287965/SRX287965.20_summits.bed INFO @ Sun, 21 Jun 2020 19:21:46: Done! pass1 - making usageList (44 chroms): 1 millis pass2 - checking and writing primary data (1819 records, 4 fields): 4 millis CompletedMACS2peakCalling