Job ID = 6454510 SRX = SRX2172428 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:27:59 prefetch.2.10.7: 1) Downloading 'SRR4252439'... 2020-06-21T09:27:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:33:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:33:31 prefetch.2.10.7: 1) 'SRR4252439' was downloaded successfully 2020-06-21T09:33:31 prefetch.2.10.7: 'SRR4252439' has 0 unresolved dependencies Read 40748256 spots for SRR4252439/SRR4252439.sra Written 40748256 spots for SRR4252439/SRR4252439.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: 00:09:37 40748256 reads; of these: 40748256 (100.00%) were unpaired; of these: 2842965 (6.98%) aligned 0 times 31480722 (77.26%) aligned exactly 1 time 6424569 (15.77%) aligned >1 times 93.02% overall alignment rate Time searching: 00:09:37 Overall time: 00:09:37 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 16 files... [bam_rmdupse_core] 14660293 / 37905291 = 0.3868 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 18:54:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.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 18:54:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:54:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:54:26: 1000000 INFO @ Sun, 21 Jun 2020 18:54:31: 2000000 INFO @ Sun, 21 Jun 2020 18:54:35: 3000000 INFO @ Sun, 21 Jun 2020 18:54:40: 4000000 INFO @ Sun, 21 Jun 2020 18:54:45: 5000000 INFO @ Sun, 21 Jun 2020 18:54:49: 6000000 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 18:54:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.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 18:54:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:54:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:54:54: 7000000 INFO @ Sun, 21 Jun 2020 18:54:56: 1000000 INFO @ Sun, 21 Jun 2020 18:54:59: 8000000 INFO @ Sun, 21 Jun 2020 18:55:01: 2000000 INFO @ Sun, 21 Jun 2020 18:55:04: 9000000 INFO @ Sun, 21 Jun 2020 18:55:06: 3000000 INFO @ Sun, 21 Jun 2020 18:55:08: 10000000 INFO @ Sun, 21 Jun 2020 18:55:11: 4000000 INFO @ Sun, 21 Jun 2020 18:55:13: 11000000 INFO @ Sun, 21 Jun 2020 18:55:15: 5000000 INFO @ Sun, 21 Jun 2020 18:55:18: 12000000 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 18:55:20: 6000000 INFO @ Sun, 21 Jun 2020 18:55:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.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 18:55:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:55:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:55:23: 13000000 INFO @ Sun, 21 Jun 2020 18:55:25: 7000000 INFO @ Sun, 21 Jun 2020 18:55:26: 1000000 INFO @ Sun, 21 Jun 2020 18:55:28: 14000000 INFO @ Sun, 21 Jun 2020 18:55:30: 8000000 INFO @ Sun, 21 Jun 2020 18:55:31: 2000000 INFO @ Sun, 21 Jun 2020 18:55:32: 15000000 INFO @ Sun, 21 Jun 2020 18:55:35: 9000000 INFO @ Sun, 21 Jun 2020 18:55:36: 3000000 INFO @ Sun, 21 Jun 2020 18:55:37: 16000000 INFO @ Sun, 21 Jun 2020 18:55:39: 10000000 INFO @ Sun, 21 Jun 2020 18:55:41: 4000000 INFO @ Sun, 21 Jun 2020 18:55:42: 17000000 INFO @ Sun, 21 Jun 2020 18:55:44: 11000000 INFO @ Sun, 21 Jun 2020 18:55:45: 5000000 INFO @ Sun, 21 Jun 2020 18:55:47: 18000000 INFO @ Sun, 21 Jun 2020 18:55:49: 12000000 INFO @ Sun, 21 Jun 2020 18:55:50: 6000000 INFO @ Sun, 21 Jun 2020 18:55:52: 19000000 INFO @ Sun, 21 Jun 2020 18:55:54: 13000000 INFO @ Sun, 21 Jun 2020 18:55:55: 7000000 INFO @ Sun, 21 Jun 2020 18:55:57: 20000000 INFO @ Sun, 21 Jun 2020 18:55:59: 14000000 INFO @ Sun, 21 Jun 2020 18:56:00: 8000000 INFO @ Sun, 21 Jun 2020 18:56:02: 21000000 INFO @ Sun, 21 Jun 2020 18:56:04: 15000000 INFO @ Sun, 21 Jun 2020 18:56:04: 9000000 INFO @ Sun, 21 Jun 2020 18:56:07: 22000000 INFO @ Sun, 21 Jun 2020 18:56:08: 16000000 INFO @ Sun, 21 Jun 2020 18:56:09: 10000000 INFO @ Sun, 21 Jun 2020 18:56:12: 23000000 INFO @ Sun, 21 Jun 2020 18:56:13: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:56:13: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:56:13: #1 total tags in treatment: 23244998 INFO @ Sun, 21 Jun 2020 18:56:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:56:13: #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 18:56:13: 17000000 INFO @ Sun, 21 Jun 2020 18:56:14: #1 tags after filtering in treatment: 23244922 INFO @ Sun, 21 Jun 2020 18:56:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:56:14: #1 finished! INFO @ Sun, 21 Jun 2020 18:56:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:56:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:56:14: 11000000 INFO @ Sun, 21 Jun 2020 18:56:16: #2 number of paired peaks: 5195 INFO @ Sun, 21 Jun 2020 18:56:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:56:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:56:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:56:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:56:16: #2 predicted fragment length is 161 bps INFO @ Sun, 21 Jun 2020 18:56:16: #2 alternative fragment length(s) may be 161 bps INFO @ Sun, 21 Jun 2020 18:56:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.05_model.r INFO @ Sun, 21 Jun 2020 18:56:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:56:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:56:18: 18000000 INFO @ Sun, 21 Jun 2020 18:56:18: 12000000 INFO @ Sun, 21 Jun 2020 18:56:23: 19000000 INFO @ Sun, 21 Jun 2020 18:56:23: 13000000 INFO @ Sun, 21 Jun 2020 18:56:28: 20000000 INFO @ Sun, 21 Jun 2020 18:56:28: 14000000 INFO @ Sun, 21 Jun 2020 18:56:32: 21000000 INFO @ Sun, 21 Jun 2020 18:56:32: 15000000 INFO @ Sun, 21 Jun 2020 18:56:37: 22000000 INFO @ Sun, 21 Jun 2020 18:56:37: 16000000 INFO @ Sun, 21 Jun 2020 18:56:42: 17000000 INFO @ Sun, 21 Jun 2020 18:56:42: 23000000 INFO @ Sun, 21 Jun 2020 18:56:43: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:56:43: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:56:43: #1 total tags in treatment: 23244998 INFO @ Sun, 21 Jun 2020 18:56:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:56:43: #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 18:56:44: #1 tags after filtering in treatment: 23244922 INFO @ Sun, 21 Jun 2020 18:56:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:56:44: #1 finished! INFO @ Sun, 21 Jun 2020 18:56:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:56:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:56:46: #2 number of paired peaks: 5195 INFO @ Sun, 21 Jun 2020 18:56:46: start model_add_line... INFO @ Sun, 21 Jun 2020 18:56:46: start X-correlation... INFO @ Sun, 21 Jun 2020 18:56:46: end of X-cor INFO @ Sun, 21 Jun 2020 18:56:46: #2 finished! INFO @ Sun, 21 Jun 2020 18:56:46: #2 predicted fragment length is 161 bps INFO @ Sun, 21 Jun 2020 18:56:46: #2 alternative fragment length(s) may be 161 bps INFO @ Sun, 21 Jun 2020 18:56:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.10_model.r INFO @ Sun, 21 Jun 2020 18:56:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:56:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:56:46: 18000000 INFO @ Sun, 21 Jun 2020 18:56:51: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:56:56: 20000000 INFO @ Sun, 21 Jun 2020 18:57:00: 21000000 INFO @ Sun, 21 Jun 2020 18:57:05: 22000000 INFO @ Sun, 21 Jun 2020 18:57:09: 23000000 INFO @ Sun, 21 Jun 2020 18:57:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:57:11: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:57:11: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:57:11: #1 total tags in treatment: 23244998 INFO @ Sun, 21 Jun 2020 18:57:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:57:11: #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 18:57:11: #1 tags after filtering in treatment: 23244922 INFO @ Sun, 21 Jun 2020 18:57:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:57:11: #1 finished! INFO @ Sun, 21 Jun 2020 18:57:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:57:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:57:13: #2 number of paired peaks: 5195 INFO @ Sun, 21 Jun 2020 18:57:13: start model_add_line... INFO @ Sun, 21 Jun 2020 18:57:14: start X-correlation... INFO @ Sun, 21 Jun 2020 18:57:14: end of X-cor INFO @ Sun, 21 Jun 2020 18:57:14: #2 finished! INFO @ Sun, 21 Jun 2020 18:57:14: #2 predicted fragment length is 161 bps INFO @ Sun, 21 Jun 2020 18:57:14: #2 alternative fragment length(s) may be 161 bps INFO @ Sun, 21 Jun 2020 18:57:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.20_model.r INFO @ Sun, 21 Jun 2020 18:57:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:57:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:57:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:57:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:57:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.05_summits.bed INFO @ Sun, 21 Jun 2020 18:57:36: Done! pass1 - making usageList (541 chroms): 3 millis pass2 - checking and writing primary data (15412 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:57:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:58:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:58:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:58:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.10_summits.bed INFO @ Sun, 21 Jun 2020 18:58:05: Done! pass1 - making usageList (412 chroms): 3 millis pass2 - checking and writing primary data (13438 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:58:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:58:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:58:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:58:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2172428/SRX2172428.20_summits.bed INFO @ Sun, 21 Jun 2020 18:58:32: Done! pass1 - making usageList (234 chroms): 3 millis pass2 - checking and writing primary data (11225 records, 4 fields): 19 millis CompletedMACS2peakCalling