Job ID = 6454029 SRX = SRX1794216 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:42:47 prefetch.2.10.7: 1) Downloading 'SRR3575247'... 2020-06-21T08:42:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:44:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:44:49 prefetch.2.10.7: 1) 'SRR3575247' was downloaded successfully 2020-06-21T08:44:49 prefetch.2.10.7: 'SRR3575247' has 0 unresolved dependencies Read 29182924 spots for SRR3575247/SRR3575247.sra Written 29182924 spots for SRR3575247/SRR3575247.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: 00:07:00 29182924 reads; of these: 29182924 (100.00%) were unpaired; of these: 8135141 (27.88%) aligned 0 times 15844552 (54.29%) aligned exactly 1 time 5203231 (17.83%) aligned >1 times 72.12% overall alignment rate Time searching: 00:07:00 Overall time: 00:07:00 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] 4801321 / 21047783 = 0.2281 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 17:57:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.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 17:57:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:57:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:58:01: 1000000 INFO @ Sun, 21 Jun 2020 17:58:06: 2000000 INFO @ Sun, 21 Jun 2020 17:58:11: 3000000 INFO @ Sun, 21 Jun 2020 17:58:17: 4000000 INFO @ Sun, 21 Jun 2020 17:58:22: 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 17:58:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.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 17:58:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:58:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:58:27: 6000000 INFO @ Sun, 21 Jun 2020 17:58:33: 1000000 INFO @ Sun, 21 Jun 2020 17:58:33: 7000000 INFO @ Sun, 21 Jun 2020 17:58:39: 8000000 INFO @ Sun, 21 Jun 2020 17:58:39: 2000000 INFO @ Sun, 21 Jun 2020 17:58:45: 9000000 INFO @ Sun, 21 Jun 2020 17:58:45: 3000000 INFO @ Sun, 21 Jun 2020 17:58:50: 10000000 INFO @ Sun, 21 Jun 2020 17:58:51: 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 17:58:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.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 17:58:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:58:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:58:56: 11000000 INFO @ Sun, 21 Jun 2020 17:58:57: 5000000 INFO @ Sun, 21 Jun 2020 17:59:02: 12000000 INFO @ Sun, 21 Jun 2020 17:59:03: 1000000 INFO @ Sun, 21 Jun 2020 17:59:03: 6000000 INFO @ Sun, 21 Jun 2020 17:59:08: 13000000 INFO @ Sun, 21 Jun 2020 17:59:09: 7000000 INFO @ Sun, 21 Jun 2020 17:59:09: 2000000 INFO @ Sun, 21 Jun 2020 17:59:14: 14000000 INFO @ Sun, 21 Jun 2020 17:59:15: 8000000 INFO @ Sun, 21 Jun 2020 17:59:16: 3000000 INFO @ Sun, 21 Jun 2020 17:59:20: 15000000 INFO @ Sun, 21 Jun 2020 17:59:21: 9000000 INFO @ Sun, 21 Jun 2020 17:59:23: 4000000 INFO @ Sun, 21 Jun 2020 17:59:26: 16000000 INFO @ Sun, 21 Jun 2020 17:59:27: 10000000 INFO @ Sun, 21 Jun 2020 17:59:28: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 17:59:28: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 17:59:28: #1 total tags in treatment: 16246462 INFO @ Sun, 21 Jun 2020 17:59:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:59:28: #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 17:59:28: #1 tags after filtering in treatment: 16246364 INFO @ Sun, 21 Jun 2020 17:59:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:59:28: #1 finished! INFO @ Sun, 21 Jun 2020 17:59:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:59:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:59:30: #2 number of paired peaks: 5085 INFO @ Sun, 21 Jun 2020 17:59:30: start model_add_line... INFO @ Sun, 21 Jun 2020 17:59:30: start X-correlation... INFO @ Sun, 21 Jun 2020 17:59:30: end of X-cor INFO @ Sun, 21 Jun 2020 17:59:30: #2 finished! INFO @ Sun, 21 Jun 2020 17:59:30: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 17:59:30: #2 alternative fragment length(s) may be 4,165 bps INFO @ Sun, 21 Jun 2020 17:59:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.05_model.r INFO @ Sun, 21 Jun 2020 17:59:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:59:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:59:30: 5000000 INFO @ Sun, 21 Jun 2020 17:59:32: 11000000 INFO @ Sun, 21 Jun 2020 17:59:37: 6000000 INFO @ Sun, 21 Jun 2020 17:59:38: 12000000 INFO @ Sun, 21 Jun 2020 17:59:43: 7000000 INFO @ Sun, 21 Jun 2020 17:59:44: 13000000 INFO @ Sun, 21 Jun 2020 17:59:50: 8000000 INFO @ Sun, 21 Jun 2020 17:59:50: 14000000 INFO @ Sun, 21 Jun 2020 17:59:56: 15000000 INFO @ Sun, 21 Jun 2020 17:59:57: 9000000 INFO @ Sun, 21 Jun 2020 18:00:02: 16000000 INFO @ Sun, 21 Jun 2020 18:00:03: 10000000 INFO @ Sun, 21 Jun 2020 18:00:03: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:00:03: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:00:03: #1 total tags in treatment: 16246462 INFO @ Sun, 21 Jun 2020 18:00:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:00:03: #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 18:00:04: #1 tags after filtering in treatment: 16246364 INFO @ Sun, 21 Jun 2020 18:00:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:00:04: #1 finished! INFO @ Sun, 21 Jun 2020 18:00:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:00:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:00:05: #2 number of paired peaks: 5085 INFO @ Sun, 21 Jun 2020 18:00:05: start model_add_line... INFO @ Sun, 21 Jun 2020 18:00:06: start X-correlation... INFO @ Sun, 21 Jun 2020 18:00:06: end of X-cor INFO @ Sun, 21 Jun 2020 18:00:06: #2 finished! INFO @ Sun, 21 Jun 2020 18:00:06: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 18:00:06: #2 alternative fragment length(s) may be 4,165 bps INFO @ Sun, 21 Jun 2020 18:00:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.10_model.r INFO @ Sun, 21 Jun 2020 18:00:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:00:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:00:10: 11000000 INFO @ Sun, 21 Jun 2020 18:00:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:00:16: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:00:22: 13000000 INFO @ Sun, 21 Jun 2020 18:00:28: 14000000 INFO @ Sun, 21 Jun 2020 18:00:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:00:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:00:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.05_summits.bed INFO @ Sun, 21 Jun 2020 18:00:30: Done! pass1 - making usageList (526 chroms): 2 millis pass2 - checking and writing primary data (12028 records, 4 fields): 55 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:00:34: 15000000 INFO @ Sun, 21 Jun 2020 18:00:41: 16000000 INFO @ Sun, 21 Jun 2020 18:00:42: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:00:42: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:00:42: #1 total tags in treatment: 16246462 INFO @ Sun, 21 Jun 2020 18:00:42: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:00:42: #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 18:00:43: #1 tags after filtering in treatment: 16246364 INFO @ Sun, 21 Jun 2020 18:00:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:00:43: #1 finished! INFO @ Sun, 21 Jun 2020 18:00:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:00:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:00:44: #2 number of paired peaks: 5085 INFO @ Sun, 21 Jun 2020 18:00:44: start model_add_line... INFO @ Sun, 21 Jun 2020 18:00:44: start X-correlation... INFO @ Sun, 21 Jun 2020 18:00:44: end of X-cor INFO @ Sun, 21 Jun 2020 18:00:44: #2 finished! INFO @ Sun, 21 Jun 2020 18:00:44: #2 predicted fragment length is 165 bps INFO @ Sun, 21 Jun 2020 18:00:44: #2 alternative fragment length(s) may be 4,165 bps INFO @ Sun, 21 Jun 2020 18:00:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.20_model.r INFO @ Sun, 21 Jun 2020 18:00:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:00:44: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:00:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:01:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:01:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:01:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.10_summits.bed INFO @ Sun, 21 Jun 2020 18:01:05: Done! pass1 - making usageList (411 chroms): 2 millis pass2 - checking and writing primary data (9197 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:01:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:01:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:01:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:01:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1794216/SRX1794216.20_summits.bed INFO @ Sun, 21 Jun 2020 18:01:43: Done! pass1 - making usageList (247 chroms): 1 millis pass2 - checking and writing primary data (5328 records, 4 fields): 12 millis CompletedMACS2peakCalling