Job ID = 6453196 SRX = SRX1078885 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:08:33 prefetch.2.10.7: 1) Downloading 'SRR2084564'... 2020-06-21T08:08:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:09:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:09:56 prefetch.2.10.7: 'SRR2084564' is valid 2020-06-21T08:09:56 prefetch.2.10.7: 1) 'SRR2084564' was downloaded successfully 2020-06-21T08:09:56 prefetch.2.10.7: 'SRR2084564' has 0 unresolved dependencies Read 6403967 spots for SRR2084564/SRR2084564.sra Written 6403967 spots for SRR2084564/SRR2084564.sra 2020-06-21T08:10:29 prefetch.2.10.7: 1) Downloading 'SRR2084565'... 2020-06-21T08:10:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:11:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:11:20 prefetch.2.10.7: 'SRR2084565' is valid 2020-06-21T08:11:20 prefetch.2.10.7: 1) 'SRR2084565' was downloaded successfully 2020-06-21T08:11:20 prefetch.2.10.7: 'SRR2084565' has 0 unresolved dependencies Read 6327624 spots for SRR2084565/SRR2084565.sra Written 6327624 spots for SRR2084565/SRR2084565.sra 2020-06-21T08:11:51 prefetch.2.10.7: 1) Downloading 'SRR2084566'... 2020-06-21T08:11:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:12:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:12:44 prefetch.2.10.7: 'SRR2084566' is valid 2020-06-21T08:12:44 prefetch.2.10.7: 1) 'SRR2084566' was downloaded successfully 2020-06-21T08:12:44 prefetch.2.10.7: 'SRR2084566' has 0 unresolved dependencies Read 6294781 spots for SRR2084566/SRR2084566.sra Written 6294781 spots for SRR2084566/SRR2084566.sra 2020-06-21T08:13:15 prefetch.2.10.7: 1) Downloading 'SRR2084567'... 2020-06-21T08:13:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:14:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:14:40 prefetch.2.10.7: 'SRR2084567' is valid 2020-06-21T08:14:40 prefetch.2.10.7: 1) 'SRR2084567' was downloaded successfully 2020-06-21T08:14:40 prefetch.2.10.7: 'SRR2084567' has 0 unresolved dependencies Read 6166756 spots for SRR2084567/SRR2084567.sra Written 6166756 spots for SRR2084567/SRR2084567.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:36 25193128 reads; of these: 25193128 (100.00%) were unpaired; of these: 3778226 (15.00%) aligned 0 times 15817261 (62.78%) aligned exactly 1 time 5597641 (22.22%) aligned >1 times 85.00% overall alignment rate Time searching: 00:06:37 Overall time: 00:06:37 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 12 files... [bam_rmdupse_core] 5598064 / 21414902 = 0.2614 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 17:27:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.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 17:27:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:27:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:27:09: 1000000 INFO @ Sun, 21 Jun 2020 17:27:14: 2000000 INFO @ Sun, 21 Jun 2020 17:27:19: 3000000 INFO @ Sun, 21 Jun 2020 17:27:24: 4000000 INFO @ Sun, 21 Jun 2020 17:27:29: 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 17:27:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.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 17:27:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:27:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:27:34: 6000000 INFO @ Sun, 21 Jun 2020 17:27:38: 1000000 INFO @ Sun, 21 Jun 2020 17:27:39: 7000000 INFO @ Sun, 21 Jun 2020 17:27:43: 2000000 INFO @ Sun, 21 Jun 2020 17:27:44: 8000000 INFO @ Sun, 21 Jun 2020 17:27:49: 3000000 INFO @ Sun, 21 Jun 2020 17:27:50: 9000000 INFO @ Sun, 21 Jun 2020 17:27:54: 4000000 INFO @ Sun, 21 Jun 2020 17:27:55: 10000000 INFO @ Sun, 21 Jun 2020 17:27:59: 5000000 INFO @ Sun, 21 Jun 2020 17:28:00: 11000000 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 17:28:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.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 17:28:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:28:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:28:04: 6000000 INFO @ Sun, 21 Jun 2020 17:28:05: 12000000 INFO @ Sun, 21 Jun 2020 17:28:08: 1000000 INFO @ Sun, 21 Jun 2020 17:28:09: 7000000 INFO @ Sun, 21 Jun 2020 17:28:10: 13000000 INFO @ Sun, 21 Jun 2020 17:28:13: 2000000 INFO @ Sun, 21 Jun 2020 17:28:14: 8000000 INFO @ Sun, 21 Jun 2020 17:28:16: 14000000 INFO @ Sun, 21 Jun 2020 17:28:19: 3000000 INFO @ Sun, 21 Jun 2020 17:28:19: 9000000 INFO @ Sun, 21 Jun 2020 17:28:21: 15000000 INFO @ Sun, 21 Jun 2020 17:28:24: 4000000 INFO @ Sun, 21 Jun 2020 17:28:25: 10000000 INFO @ Sun, 21 Jun 2020 17:28:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:28:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:28:26: #1 total tags in treatment: 15816838 INFO @ Sun, 21 Jun 2020 17:28:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:28:26: #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 17:28:26: #1 tags after filtering in treatment: 15816757 INFO @ Sun, 21 Jun 2020 17:28:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:28:26: #1 finished! INFO @ Sun, 21 Jun 2020 17:28:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:28:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:28:28: #2 number of paired peaks: 5762 INFO @ Sun, 21 Jun 2020 17:28:28: start model_add_line... INFO @ Sun, 21 Jun 2020 17:28:28: start X-correlation... INFO @ Sun, 21 Jun 2020 17:28:28: end of X-cor INFO @ Sun, 21 Jun 2020 17:28:28: #2 finished! INFO @ Sun, 21 Jun 2020 17:28:28: #2 predicted fragment length is 166 bps INFO @ Sun, 21 Jun 2020 17:28:28: #2 alternative fragment length(s) may be 166 bps INFO @ Sun, 21 Jun 2020 17:28:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.05_model.r INFO @ Sun, 21 Jun 2020 17:28:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:28:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:28:29: 5000000 INFO @ Sun, 21 Jun 2020 17:28:30: 11000000 INFO @ Sun, 21 Jun 2020 17:28:34: 6000000 INFO @ Sun, 21 Jun 2020 17:28:35: 12000000 INFO @ Sun, 21 Jun 2020 17:28:39: 7000000 INFO @ Sun, 21 Jun 2020 17:28:40: 13000000 INFO @ Sun, 21 Jun 2020 17:28:44: 8000000 INFO @ Sun, 21 Jun 2020 17:28:45: 14000000 INFO @ Sun, 21 Jun 2020 17:28:49: 9000000 INFO @ Sun, 21 Jun 2020 17:28:51: 15000000 INFO @ Sun, 21 Jun 2020 17:28:54: 10000000 INFO @ Sun, 21 Jun 2020 17:28:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:28:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:28:55: #1 total tags in treatment: 15816838 INFO @ Sun, 21 Jun 2020 17:28:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:28:55: #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 17:28:56: #1 tags after filtering in treatment: 15816757 INFO @ Sun, 21 Jun 2020 17:28:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:28:56: #1 finished! INFO @ Sun, 21 Jun 2020 17:28:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:28:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:28:57: #2 number of paired peaks: 5762 INFO @ Sun, 21 Jun 2020 17:28:57: start model_add_line... INFO @ Sun, 21 Jun 2020 17:28:57: start X-correlation... INFO @ Sun, 21 Jun 2020 17:28:57: end of X-cor INFO @ Sun, 21 Jun 2020 17:28:57: #2 finished! INFO @ Sun, 21 Jun 2020 17:28:57: #2 predicted fragment length is 166 bps INFO @ Sun, 21 Jun 2020 17:28:57: #2 alternative fragment length(s) may be 166 bps INFO @ Sun, 21 Jun 2020 17:28:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.10_model.r INFO @ Sun, 21 Jun 2020 17:28:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:28:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:28:59: 11000000 INFO @ Sun, 21 Jun 2020 17:29:04: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:29:09: 13000000 INFO @ Sun, 21 Jun 2020 17:29:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:29:14: 14000000 INFO @ Sun, 21 Jun 2020 17:29:19: 15000000 INFO @ Sun, 21 Jun 2020 17:29:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:29:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:29:23: #1 total tags in treatment: 15816838 INFO @ Sun, 21 Jun 2020 17:29:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:29:23: #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 17:29:24: #1 tags after filtering in treatment: 15816757 INFO @ Sun, 21 Jun 2020 17:29:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:29:24: #1 finished! INFO @ Sun, 21 Jun 2020 17:29:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:29:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:29:26: #2 number of paired peaks: 5762 INFO @ Sun, 21 Jun 2020 17:29:26: start model_add_line... INFO @ Sun, 21 Jun 2020 17:29:26: start X-correlation... INFO @ Sun, 21 Jun 2020 17:29:26: end of X-cor INFO @ Sun, 21 Jun 2020 17:29:26: #2 finished! INFO @ Sun, 21 Jun 2020 17:29:26: #2 predicted fragment length is 166 bps INFO @ Sun, 21 Jun 2020 17:29:26: #2 alternative fragment length(s) may be 166 bps INFO @ Sun, 21 Jun 2020 17:29:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.20_model.r INFO @ Sun, 21 Jun 2020 17:29:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:29:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:29:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:29:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:29:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.05_summits.bed INFO @ Sun, 21 Jun 2020 17:29:31: Done! pass1 - making usageList (564 chroms): 3 millis pass2 - checking and writing primary data (9933 records, 4 fields): 34 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:29:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:30:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:30:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:30:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.10_summits.bed INFO @ Sun, 21 Jun 2020 17:30:01: Done! pass1 - making usageList (486 chroms): 2 millis pass2 - checking and writing primary data (8129 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:30:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:30:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:30:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:30:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1078885/SRX1078885.20_summits.bed INFO @ Sun, 21 Jun 2020 17:30:27: Done! pass1 - making usageList (298 chroms): 1 millis pass2 - checking and writing primary data (5725 records, 4 fields): 14 millis CompletedMACS2peakCalling