Job ID = 6454054 SRX = SRX1794238 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:55:49 prefetch.2.10.7: 1) Downloading 'SRR3575280'... 2020-06-21T08:55:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:58:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:58:34 prefetch.2.10.7: 'SRR3575280' is valid 2020-06-21T08:58:34 prefetch.2.10.7: 1) 'SRR3575280' was downloaded successfully Read 11251283 spots for SRR3575280/SRR3575280.sra Written 11251283 spots for SRR3575280/SRR3575280.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: 00:02:45 11251283 reads; of these: 11251283 (100.00%) were unpaired; of these: 488790 (4.34%) aligned 0 times 8806764 (78.27%) aligned exactly 1 time 1955729 (17.38%) aligned >1 times 95.66% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 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] 1294862 / 10762493 = 0.1203 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 18:06:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.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 18:06:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:09: 1000000 INFO @ Sun, 21 Jun 2020 18:06:14: 2000000 INFO @ Sun, 21 Jun 2020 18:06:19: 3000000 INFO @ Sun, 21 Jun 2020 18:06:24: 4000000 INFO @ Sun, 21 Jun 2020 18:06:29: 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 18:06:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.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 18:06:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:06:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:06:34: 6000000 INFO @ Sun, 21 Jun 2020 18:06:39: 1000000 INFO @ Sun, 21 Jun 2020 18:06:40: 7000000 INFO @ Sun, 21 Jun 2020 18:06:45: 2000000 INFO @ Sun, 21 Jun 2020 18:06:45: 8000000 INFO @ Sun, 21 Jun 2020 18:06:50: 3000000 INFO @ Sun, 21 Jun 2020 18:06:51: 9000000 INFO @ Sun, 21 Jun 2020 18:06:53: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:06:53: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:06:53: #1 total tags in treatment: 9467631 INFO @ Sun, 21 Jun 2020 18:06:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:06:53: #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 18:06:54: #1 tags after filtering in treatment: 9467438 INFO @ Sun, 21 Jun 2020 18:06:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:06:54: #1 finished! INFO @ Sun, 21 Jun 2020 18:06:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:06:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:06:55: 4000000 INFO @ Sun, 21 Jun 2020 18:06:55: #2 number of paired peaks: 9093 INFO @ Sun, 21 Jun 2020 18:06:55: start model_add_line... INFO @ Sun, 21 Jun 2020 18:06:55: start X-correlation... INFO @ Sun, 21 Jun 2020 18:06:55: end of X-cor INFO @ Sun, 21 Jun 2020 18:06:55: #2 finished! INFO @ Sun, 21 Jun 2020 18:06:55: #2 predicted fragment length is 164 bps INFO @ Sun, 21 Jun 2020 18:06:55: #2 alternative fragment length(s) may be 164 bps INFO @ Sun, 21 Jun 2020 18:06:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.05_model.r INFO @ Sun, 21 Jun 2020 18:06:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:06:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:07:00: 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 18:07:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.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 18:07:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:07:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:07:05: 6000000 INFO @ Sun, 21 Jun 2020 18:07:09: 1000000 INFO @ Sun, 21 Jun 2020 18:07:11: 7000000 INFO @ Sun, 21 Jun 2020 18:07:15: 2000000 INFO @ Sun, 21 Jun 2020 18:07:17: 8000000 INFO @ Sun, 21 Jun 2020 18:07:20: 3000000 INFO @ Sun, 21 Jun 2020 18:07:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:07:22: 9000000 INFO @ Sun, 21 Jun 2020 18:07:25: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:07:25: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:07:25: #1 total tags in treatment: 9467631 INFO @ Sun, 21 Jun 2020 18:07:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:25: #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 18:07:25: 4000000 INFO @ Sun, 21 Jun 2020 18:07:25: #1 tags after filtering in treatment: 9467438 INFO @ Sun, 21 Jun 2020 18:07:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:25: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:27: #2 number of paired peaks: 9093 INFO @ Sun, 21 Jun 2020 18:07:27: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:27: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:27: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:27: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:27: #2 predicted fragment length is 164 bps INFO @ Sun, 21 Jun 2020 18:07:27: #2 alternative fragment length(s) may be 164 bps INFO @ Sun, 21 Jun 2020 18:07:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.10_model.r INFO @ Sun, 21 Jun 2020 18:07:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:07:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:07:30: 5000000 INFO @ Sun, 21 Jun 2020 18:07:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:07:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:07:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.05_summits.bed INFO @ Sun, 21 Jun 2020 18:07:32: Done! pass1 - making usageList (219 chroms): 3 millis pass2 - checking and writing primary data (9739 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:07:36: 6000000 INFO @ Sun, 21 Jun 2020 18:07:41: 7000000 INFO @ Sun, 21 Jun 2020 18:07:46: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:07:52: 9000000 INFO @ Sun, 21 Jun 2020 18:07:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:07:54: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:07:54: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:07:54: #1 total tags in treatment: 9467631 INFO @ Sun, 21 Jun 2020 18:07:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:07:54: #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 18:07:55: #1 tags after filtering in treatment: 9467438 INFO @ Sun, 21 Jun 2020 18:07:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:07:55: #1 finished! INFO @ Sun, 21 Jun 2020 18:07:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:07:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:07:56: #2 number of paired peaks: 9093 INFO @ Sun, 21 Jun 2020 18:07:56: start model_add_line... INFO @ Sun, 21 Jun 2020 18:07:57: start X-correlation... INFO @ Sun, 21 Jun 2020 18:07:57: end of X-cor INFO @ Sun, 21 Jun 2020 18:07:57: #2 finished! INFO @ Sun, 21 Jun 2020 18:07:57: #2 predicted fragment length is 164 bps INFO @ Sun, 21 Jun 2020 18:07:57: #2 alternative fragment length(s) may be 164 bps INFO @ Sun, 21 Jun 2020 18:07:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.20_model.r INFO @ Sun, 21 Jun 2020 18:07:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:07:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:08:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:08:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:08:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.10_summits.bed INFO @ Sun, 21 Jun 2020 18:08:03: Done! pass1 - making usageList (158 chroms): 2 millis pass2 - checking and writing primary data (7559 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:08:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:08:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:08:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:08:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794238/SRX1794238.20_summits.bed INFO @ Sun, 21 Jun 2020 18:08:33: Done! pass1 - making usageList (97 chroms): 2 millis pass2 - checking and writing primary data (4187 records, 4 fields): 11 millis CompletedMACS2peakCalling