Job ID = 6453752 SRX = SRX1433396 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:39:33 prefetch.2.10.7: 1) Downloading 'SRR2919812'... 2020-06-21T08:39:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:43:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:43:54 prefetch.2.10.7: 1) 'SRR2919812' was downloaded successfully Read 34677956 spots for SRR2919812/SRR2919812.sra Written 34677956 spots for SRR2919812/SRR2919812.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: 00:07:23 34677956 reads; of these: 34677956 (100.00%) were unpaired; of these: 4199575 (12.11%) aligned 0 times 22654940 (65.33%) aligned exactly 1 time 7823441 (22.56%) aligned >1 times 87.89% overall alignment rate Time searching: 00:07:23 Overall time: 00:07:23 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] 12123164 / 30478381 = 0.3978 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 17:58:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.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 17:58:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:58:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:58:27: 1000000 INFO @ Sun, 21 Jun 2020 17:58:32: 2000000 INFO @ Sun, 21 Jun 2020 17:58:38: 3000000 INFO @ Sun, 21 Jun 2020 17:58:44: 4000000 INFO @ Sun, 21 Jun 2020 17:58:49: 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 17:58:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.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 17:58:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:58:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:58:54: 6000000 INFO @ Sun, 21 Jun 2020 17:58:59: 1000000 INFO @ Sun, 21 Jun 2020 17:59:00: 7000000 INFO @ Sun, 21 Jun 2020 17:59:04: 2000000 INFO @ Sun, 21 Jun 2020 17:59:06: 8000000 INFO @ Sun, 21 Jun 2020 17:59:10: 3000000 INFO @ Sun, 21 Jun 2020 17:59:11: 9000000 INFO @ Sun, 21 Jun 2020 17:59:16: 4000000 INFO @ Sun, 21 Jun 2020 17:59:17: 10000000 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 17:59:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.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 17:59:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:59:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:59:21: 5000000 INFO @ Sun, 21 Jun 2020 17:59:22: 11000000 INFO @ Sun, 21 Jun 2020 17:59:27: 1000000 INFO @ Sun, 21 Jun 2020 17:59:27: 6000000 INFO @ Sun, 21 Jun 2020 17:59:28: 12000000 INFO @ Sun, 21 Jun 2020 17:59:33: 7000000 INFO @ Sun, 21 Jun 2020 17:59:33: 2000000 INFO @ Sun, 21 Jun 2020 17:59:34: 13000000 INFO @ Sun, 21 Jun 2020 17:59:38: 8000000 INFO @ Sun, 21 Jun 2020 17:59:38: 3000000 INFO @ Sun, 21 Jun 2020 17:59:39: 14000000 INFO @ Sun, 21 Jun 2020 17:59:44: 9000000 INFO @ Sun, 21 Jun 2020 17:59:44: 4000000 INFO @ Sun, 21 Jun 2020 17:59:45: 15000000 INFO @ Sun, 21 Jun 2020 17:59:50: 5000000 INFO @ Sun, 21 Jun 2020 17:59:50: 10000000 INFO @ Sun, 21 Jun 2020 17:59:51: 16000000 INFO @ Sun, 21 Jun 2020 17:59:55: 6000000 INFO @ Sun, 21 Jun 2020 17:59:56: 11000000 INFO @ Sun, 21 Jun 2020 17:59:57: 17000000 INFO @ Sun, 21 Jun 2020 18:00:01: 7000000 INFO @ Sun, 21 Jun 2020 18:00:01: 12000000 INFO @ Sun, 21 Jun 2020 18:00:02: 18000000 INFO @ Sun, 21 Jun 2020 18:00:05: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:00:05: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:00:05: #1 total tags in treatment: 18355217 INFO @ Sun, 21 Jun 2020 18:00:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:00:05: #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 18:00:05: #1 tags after filtering in treatment: 18355163 INFO @ Sun, 21 Jun 2020 18:00:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:00:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:00:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:00:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:00:06: #2 number of paired peaks: 1006 INFO @ Sun, 21 Jun 2020 18:00:06: start model_add_line... INFO @ Sun, 21 Jun 2020 18:00:07: start X-correlation... INFO @ Sun, 21 Jun 2020 18:00:07: end of X-cor INFO @ Sun, 21 Jun 2020 18:00:07: #2 finished! INFO @ Sun, 21 Jun 2020 18:00:07: #2 predicted fragment length is 113 bps INFO @ Sun, 21 Jun 2020 18:00:07: #2 alternative fragment length(s) may be 4,113 bps INFO @ Sun, 21 Jun 2020 18:00:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.05_model.r INFO @ Sun, 21 Jun 2020 18:00:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:00:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:00:07: 8000000 INFO @ Sun, 21 Jun 2020 18:00:07: 13000000 INFO @ Sun, 21 Jun 2020 18:00:12: 9000000 INFO @ Sun, 21 Jun 2020 18:00:13: 14000000 INFO @ Sun, 21 Jun 2020 18:00:18: 10000000 INFO @ Sun, 21 Jun 2020 18:00:18: 15000000 INFO @ Sun, 21 Jun 2020 18:00:24: 11000000 INFO @ Sun, 21 Jun 2020 18:00:24: 16000000 INFO @ Sun, 21 Jun 2020 18:00:29: 12000000 INFO @ Sun, 21 Jun 2020 18:00:30: 17000000 INFO @ Sun, 21 Jun 2020 18:00:35: 13000000 INFO @ Sun, 21 Jun 2020 18:00:36: 18000000 INFO @ Sun, 21 Jun 2020 18:00:38: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:00:38: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:00:38: #1 total tags in treatment: 18355217 INFO @ Sun, 21 Jun 2020 18:00:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:00:38: #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 18:00:38: #1 tags after filtering in treatment: 18355163 INFO @ Sun, 21 Jun 2020 18:00:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:00:38: #1 finished! INFO @ Sun, 21 Jun 2020 18:00:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:00:38: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:00:40: #2 number of paired peaks: 1006 INFO @ Sun, 21 Jun 2020 18:00:40: start model_add_line... INFO @ Sun, 21 Jun 2020 18:00:40: start X-correlation... INFO @ Sun, 21 Jun 2020 18:00:40: end of X-cor INFO @ Sun, 21 Jun 2020 18:00:40: #2 finished! INFO @ Sun, 21 Jun 2020 18:00:40: #2 predicted fragment length is 113 bps INFO @ Sun, 21 Jun 2020 18:00:40: #2 alternative fragment length(s) may be 4,113 bps INFO @ Sun, 21 Jun 2020 18:00:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.10_model.r INFO @ Sun, 21 Jun 2020 18:00:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:00:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:00:40: 14000000 INFO @ Sun, 21 Jun 2020 18:00:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:00:46: 15000000 INFO @ Sun, 21 Jun 2020 18:00:51: 16000000 INFO @ Sun, 21 Jun 2020 18:00:56: 17000000 INFO @ Sun, 21 Jun 2020 18:01:01: 18000000 INFO @ Sun, 21 Jun 2020 18:01:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:01:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:01:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.05_summits.bed INFO @ Sun, 21 Jun 2020 18:01:02: Done! pass1 - making usageList (746 chroms): 2 millis pass2 - checking and writing primary data (5531 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:01:03: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 18:01:03: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 18:01:03: #1 total tags in treatment: 18355217 INFO @ Sun, 21 Jun 2020 18:01:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:01:03: #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 18:01:04: #1 tags after filtering in treatment: 18355163 INFO @ Sun, 21 Jun 2020 18:01:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:01:04: #1 finished! INFO @ Sun, 21 Jun 2020 18:01:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:01:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:01:05: #2 number of paired peaks: 1006 INFO @ Sun, 21 Jun 2020 18:01:05: start model_add_line... INFO @ Sun, 21 Jun 2020 18:01:05: start X-correlation... INFO @ Sun, 21 Jun 2020 18:01:05: end of X-cor INFO @ Sun, 21 Jun 2020 18:01:05: #2 finished! INFO @ Sun, 21 Jun 2020 18:01:05: #2 predicted fragment length is 113 bps INFO @ Sun, 21 Jun 2020 18:01:05: #2 alternative fragment length(s) may be 4,113 bps INFO @ Sun, 21 Jun 2020 18:01:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.20_model.r INFO @ Sun, 21 Jun 2020 18:01:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:01:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:01:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:01:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:01:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:01:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.10_summits.bed INFO @ Sun, 21 Jun 2020 18:01:36: Done! pass1 - making usageList (612 chroms): 1 millis pass2 - checking and writing primary data (3543 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:01:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:02:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:02:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:02:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433396/SRX1433396.20_summits.bed INFO @ Sun, 21 Jun 2020 18:02:02: Done! pass1 - making usageList (347 chroms): 1 millis pass2 - checking and writing primary data (1503 records, 4 fields): 12 millis CompletedMACS2peakCalling