Job ID = 6453432 SRX = SRX1134707 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:16:49 prefetch.2.10.7: 1) Downloading 'SRR2147088'... 2020-06-21T08:16:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:20:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:20:23 prefetch.2.10.7: 1) 'SRR2147088' was downloaded successfully 2020-06-21T08:20:23 prefetch.2.10.7: 'SRR2147088' has 0 unresolved dependencies Read 18980532 spots for SRR2147088/SRR2147088.sra Written 18980532 spots for SRR2147088/SRR2147088.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: 00:03:54 18980532 reads; of these: 18980532 (100.00%) were unpaired; of these: 1612977 (8.50%) aligned 0 times 15211939 (80.14%) aligned exactly 1 time 2155616 (11.36%) aligned >1 times 91.50% overall alignment rate Time searching: 00:03:54 Overall time: 00:03:54 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] 9249089 / 17367555 = 0.5325 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 17:29:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.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 17:29:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:29:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:29:19: 1000000 INFO @ Sun, 21 Jun 2020 17:29:26: 2000000 INFO @ Sun, 21 Jun 2020 17:29:32: 3000000 INFO @ Sun, 21 Jun 2020 17:29:39: 4000000 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 17:29:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.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 17:29:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:29:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:29:46: 5000000 INFO @ Sun, 21 Jun 2020 17:29:50: 1000000 INFO @ Sun, 21 Jun 2020 17:29:52: 6000000 INFO @ Sun, 21 Jun 2020 17:29:57: 2000000 INFO @ Sun, 21 Jun 2020 17:30:00: 7000000 INFO @ Sun, 21 Jun 2020 17:30:03: 3000000 INFO @ Sun, 21 Jun 2020 17:30:07: 8000000 INFO @ Sun, 21 Jun 2020 17:30:08: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:30:08: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:30:08: #1 total tags in treatment: 8118466 INFO @ Sun, 21 Jun 2020 17:30:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:30:08: #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 17:30:08: #1 tags after filtering in treatment: 8118295 INFO @ Sun, 21 Jun 2020 17:30:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:30:08: #1 finished! INFO @ Sun, 21 Jun 2020 17:30:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:30:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:30:09: #2 number of paired peaks: 3696 INFO @ Sun, 21 Jun 2020 17:30:09: start model_add_line... INFO @ Sun, 21 Jun 2020 17:30:09: start X-correlation... INFO @ Sun, 21 Jun 2020 17:30:09: end of X-cor INFO @ Sun, 21 Jun 2020 17:30:09: #2 finished! INFO @ Sun, 21 Jun 2020 17:30:09: #2 predicted fragment length is 211 bps INFO @ Sun, 21 Jun 2020 17:30:09: #2 alternative fragment length(s) may be 211 bps INFO @ Sun, 21 Jun 2020 17:30:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.05_model.r INFO @ Sun, 21 Jun 2020 17:30:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:30:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:30:10: 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 17:30:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.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 17:30:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:30:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:30:17: 5000000 INFO @ Sun, 21 Jun 2020 17:30:20: 1000000 INFO @ Sun, 21 Jun 2020 17:30:24: 6000000 INFO @ Sun, 21 Jun 2020 17:30:27: 2000000 INFO @ Sun, 21 Jun 2020 17:30:31: 7000000 INFO @ Sun, 21 Jun 2020 17:30:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:30:34: 3000000 INFO @ Sun, 21 Jun 2020 17:30:38: 8000000 INFO @ Sun, 21 Jun 2020 17:30:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:30:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:30:39: #1 total tags in treatment: 8118466 INFO @ Sun, 21 Jun 2020 17:30:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:30:39: #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 17:30:39: #1 tags after filtering in treatment: 8118295 INFO @ Sun, 21 Jun 2020 17:30:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:30:39: #1 finished! INFO @ Sun, 21 Jun 2020 17:30:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:30:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:30:40: #2 number of paired peaks: 3696 INFO @ Sun, 21 Jun 2020 17:30:40: start model_add_line... INFO @ Sun, 21 Jun 2020 17:30:40: start X-correlation... INFO @ Sun, 21 Jun 2020 17:30:40: end of X-cor INFO @ Sun, 21 Jun 2020 17:30:40: #2 finished! INFO @ Sun, 21 Jun 2020 17:30:40: #2 predicted fragment length is 211 bps INFO @ Sun, 21 Jun 2020 17:30:40: #2 alternative fragment length(s) may be 211 bps INFO @ Sun, 21 Jun 2020 17:30:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.10_model.r INFO @ Sun, 21 Jun 2020 17:30:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:30:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:30:42: 4000000 INFO @ Sun, 21 Jun 2020 17:30:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:30:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:30:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.05_summits.bed INFO @ Sun, 21 Jun 2020 17:30:44: Done! pass1 - making usageList (126 chroms): 1 millis pass2 - checking and writing primary data (5151 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:30:48: 5000000 INFO @ Sun, 21 Jun 2020 17:30:55: 6000000 INFO @ Sun, 21 Jun 2020 17:31:02: 7000000 INFO @ Sun, 21 Jun 2020 17:31:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:31:09: 8000000 INFO @ Sun, 21 Jun 2020 17:31:10: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:31:10: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:31:10: #1 total tags in treatment: 8118466 INFO @ Sun, 21 Jun 2020 17:31:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:31:10: #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 17:31:10: #1 tags after filtering in treatment: 8118295 INFO @ Sun, 21 Jun 2020 17:31:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:31:10: #1 finished! INFO @ Sun, 21 Jun 2020 17:31:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:31:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:31:11: #2 number of paired peaks: 3696 INFO @ Sun, 21 Jun 2020 17:31:11: start model_add_line... INFO @ Sun, 21 Jun 2020 17:31:11: start X-correlation... INFO @ Sun, 21 Jun 2020 17:31:11: end of X-cor INFO @ Sun, 21 Jun 2020 17:31:11: #2 finished! INFO @ Sun, 21 Jun 2020 17:31:11: #2 predicted fragment length is 211 bps INFO @ Sun, 21 Jun 2020 17:31:11: #2 alternative fragment length(s) may be 211 bps INFO @ Sun, 21 Jun 2020 17:31:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.20_model.r INFO @ Sun, 21 Jun 2020 17:31:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:31:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:31:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:31:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:31:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.10_summits.bed INFO @ Sun, 21 Jun 2020 17:31:17: Done! pass1 - making usageList (96 chroms): 2 millis pass2 - checking and writing primary data (3832 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:31:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:31:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:31:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:31:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1134707/SRX1134707.20_summits.bed INFO @ Sun, 21 Jun 2020 17:31:44: Done! pass1 - making usageList (71 chroms): 1 millis pass2 - checking and writing primary data (2714 records, 4 fields): 7 millis CompletedMACS2peakCalling