Job ID = 6455475 SRX = SRX287815 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:17:21 prefetch.2.10.7: 1) Downloading 'SRR870004'... 2020-06-21T10:17:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:19:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:19:29 prefetch.2.10.7: 'SRR870004' is valid 2020-06-21T10:19:29 prefetch.2.10.7: 1) 'SRR870004' was downloaded successfully Read 11164185 spots for SRR870004/SRR870004.sra Written 11164185 spots for SRR870004/SRR870004.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: 00:02:41 11164185 reads; of these: 11164185 (100.00%) were unpaired; of these: 381091 (3.41%) aligned 0 times 9478080 (84.90%) aligned exactly 1 time 1305014 (11.69%) aligned >1 times 96.59% overall alignment rate Time searching: 00:02:41 Overall time: 00:02:41 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] 1661236 / 10783094 = 0.1541 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 19:25:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.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 19:25:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:25:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:25:46: 1000000 INFO @ Sun, 21 Jun 2020 19:25:51: 2000000 INFO @ Sun, 21 Jun 2020 19:25:56: 3000000 INFO @ Sun, 21 Jun 2020 19:26:01: 4000000 INFO @ Sun, 21 Jun 2020 19:26:06: 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 19:26:11: 6000000 INFO @ Sun, 21 Jun 2020 19:26:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.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 19:26:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:26:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:26:16: 7000000 INFO @ Sun, 21 Jun 2020 19:26:17: 1000000 INFO @ Sun, 21 Jun 2020 19:26:22: 2000000 INFO @ Sun, 21 Jun 2020 19:26:22: 8000000 INFO @ Sun, 21 Jun 2020 19:26:27: 3000000 INFO @ Sun, 21 Jun 2020 19:26:28: 9000000 INFO @ Sun, 21 Jun 2020 19:26:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:26:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:26:28: #1 total tags in treatment: 9121858 INFO @ Sun, 21 Jun 2020 19:26:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:26:28: #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 19:26:29: #1 tags after filtering in treatment: 9121841 INFO @ Sun, 21 Jun 2020 19:26:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:26:29: #1 finished! INFO @ Sun, 21 Jun 2020 19:26:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:26:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:26:30: #2 number of paired peaks: 9984 INFO @ Sun, 21 Jun 2020 19:26:30: start model_add_line... INFO @ Sun, 21 Jun 2020 19:26:30: start X-correlation... INFO @ Sun, 21 Jun 2020 19:26:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:26:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:26:30: #2 predicted fragment length is 216 bps INFO @ Sun, 21 Jun 2020 19:26:30: #2 alternative fragment length(s) may be 3,216 bps INFO @ Sun, 21 Jun 2020 19:26:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.05_model.r INFO @ Sun, 21 Jun 2020 19:26:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:26:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:26:33: 4000000 INFO @ Sun, 21 Jun 2020 19:26:38: 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 19:26:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.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 19:26:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:26:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:26:43: 6000000 INFO @ Sun, 21 Jun 2020 19:26:47: 1000000 INFO @ Sun, 21 Jun 2020 19:26:48: 7000000 INFO @ Sun, 21 Jun 2020 19:26:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:26:52: 2000000 INFO @ Sun, 21 Jun 2020 19:26:54: 8000000 INFO @ Sun, 21 Jun 2020 19:26:57: 3000000 INFO @ Sun, 21 Jun 2020 19:26:59: 9000000 INFO @ Sun, 21 Jun 2020 19:27:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:27:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:27:00: #1 total tags in treatment: 9121858 INFO @ Sun, 21 Jun 2020 19:27:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:27:00: #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 19:27:00: #1 tags after filtering in treatment: 9121841 INFO @ Sun, 21 Jun 2020 19:27:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:27:00: #1 finished! INFO @ Sun, 21 Jun 2020 19:27:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:27:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:27:02: #2 number of paired peaks: 9984 INFO @ Sun, 21 Jun 2020 19:27:02: start model_add_line... INFO @ Sun, 21 Jun 2020 19:27:02: start X-correlation... INFO @ Sun, 21 Jun 2020 19:27:02: end of X-cor INFO @ Sun, 21 Jun 2020 19:27:02: #2 finished! INFO @ Sun, 21 Jun 2020 19:27:02: #2 predicted fragment length is 216 bps INFO @ Sun, 21 Jun 2020 19:27:02: #2 alternative fragment length(s) may be 3,216 bps INFO @ Sun, 21 Jun 2020 19:27:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.10_model.r INFO @ Sun, 21 Jun 2020 19:27:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:27:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:27:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:27:03: 4000000 INFO @ Sun, 21 Jun 2020 19:27:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:27:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.05_summits.bed INFO @ Sun, 21 Jun 2020 19:27:03: Done! pass1 - making usageList (123 chroms): 2 millis pass2 - checking and writing primary data (7802 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:27:08: 5000000 INFO @ Sun, 21 Jun 2020 19:27:13: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:27:18: 7000000 INFO @ Sun, 21 Jun 2020 19:27:24: 8000000 INFO @ Sun, 21 Jun 2020 19:27:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:27:29: 9000000 INFO @ Sun, 21 Jun 2020 19:27:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:27:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:27:29: #1 total tags in treatment: 9121858 INFO @ Sun, 21 Jun 2020 19:27:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:27:29: #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 19:27:30: #1 tags after filtering in treatment: 9121841 INFO @ Sun, 21 Jun 2020 19:27:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:27:30: #1 finished! INFO @ Sun, 21 Jun 2020 19:27:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:27:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:27:31: #2 number of paired peaks: 9984 INFO @ Sun, 21 Jun 2020 19:27:31: start model_add_line... INFO @ Sun, 21 Jun 2020 19:27:31: start X-correlation... INFO @ Sun, 21 Jun 2020 19:27:31: end of X-cor INFO @ Sun, 21 Jun 2020 19:27:31: #2 finished! INFO @ Sun, 21 Jun 2020 19:27:31: #2 predicted fragment length is 216 bps INFO @ Sun, 21 Jun 2020 19:27:31: #2 alternative fragment length(s) may be 3,216 bps INFO @ Sun, 21 Jun 2020 19:27:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.20_model.r INFO @ Sun, 21 Jun 2020 19:27:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:27:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:27:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:27:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:27:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.10_summits.bed INFO @ Sun, 21 Jun 2020 19:27:37: Done! pass1 - making usageList (91 chroms): 1 millis pass2 - checking and writing primary data (4734 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:27:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:28:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:28:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:28:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287815/SRX287815.20_summits.bed INFO @ Sun, 21 Jun 2020 19:28:05: Done! pass1 - making usageList (70 chroms): 0 millis pass2 - checking and writing primary data (1755 records, 4 fields): 6 millis CompletedMACS2peakCalling