Job ID = 6453868 SRX = SRX1537617 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:40:02 prefetch.2.10.7: 1) Downloading 'SRR3109312'... 2020-06-21T08:40:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:42:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:42:40 prefetch.2.10.7: 'SRR3109312' is valid 2020-06-21T08:42:40 prefetch.2.10.7: 1) 'SRR3109312' was downloaded successfully Read 11450650 spots for SRR3109312/SRR3109312.sra Written 11450650 spots for SRR3109312/SRR3109312.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: 00:03:25 11450650 reads; of these: 11450650 (100.00%) were unpaired; of these: 1531722 (13.38%) aligned 0 times 6723920 (58.72%) aligned exactly 1 time 3195008 (27.90%) aligned >1 times 86.62% overall alignment rate Time searching: 00:03:25 Overall time: 00:03:25 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] 2662196 / 9918928 = 0.2684 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 17:49:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.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 17:49:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:49:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:49:35: 1000000 INFO @ Sun, 21 Jun 2020 17:49:41: 2000000 INFO @ Sun, 21 Jun 2020 17:49:46: 3000000 INFO @ Sun, 21 Jun 2020 17:49:51: 4000000 INFO @ Sun, 21 Jun 2020 17:49:56: 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 17:50:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.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 17:50:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:50:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:50:02: 6000000 INFO @ Sun, 21 Jun 2020 17:50:06: 1000000 INFO @ Sun, 21 Jun 2020 17:50:08: 7000000 INFO @ Sun, 21 Jun 2020 17:50:10: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:50:10: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:50:10: #1 total tags in treatment: 7256732 INFO @ Sun, 21 Jun 2020 17:50:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:50:10: #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 17:50:10: #1 tags after filtering in treatment: 7256730 INFO @ Sun, 21 Jun 2020 17:50:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:50:10: #1 finished! INFO @ Sun, 21 Jun 2020 17:50:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:50:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:50:11: #2 number of paired peaks: 1160 INFO @ Sun, 21 Jun 2020 17:50:11: start model_add_line... INFO @ Sun, 21 Jun 2020 17:50:11: start X-correlation... INFO @ Sun, 21 Jun 2020 17:50:11: end of X-cor INFO @ Sun, 21 Jun 2020 17:50:11: #2 finished! INFO @ Sun, 21 Jun 2020 17:50:11: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 17:50:11: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 17:50:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.05_model.r INFO @ Sun, 21 Jun 2020 17:50:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:50:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:50:12: 2000000 INFO @ Sun, 21 Jun 2020 17:50:18: 3000000 INFO @ Sun, 21 Jun 2020 17:50:24: 4000000 INFO @ Sun, 21 Jun 2020 17:50:27: #3 Call peaks for each chromosome... 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 17:50:29: 5000000 INFO @ Sun, 21 Jun 2020 17:50:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.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 17:50:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:50:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:50:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:50:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:50:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.05_summits.bed INFO @ Sun, 21 Jun 2020 17:50:35: Done! pass1 - making usageList (681 chroms): 1 millis pass2 - checking and writing primary data (1588 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:50:35: 6000000 INFO @ Sun, 21 Jun 2020 17:50:36: 1000000 INFO @ Sun, 21 Jun 2020 17:50:41: 7000000 INFO @ Sun, 21 Jun 2020 17:50:41: 2000000 INFO @ Sun, 21 Jun 2020 17:50:43: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:50:43: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:50:43: #1 total tags in treatment: 7256732 INFO @ Sun, 21 Jun 2020 17:50:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:50:43: #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 17:50:43: #1 tags after filtering in treatment: 7256730 INFO @ Sun, 21 Jun 2020 17:50:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:50:43: #1 finished! INFO @ Sun, 21 Jun 2020 17:50:43: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:50:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:50:44: #2 number of paired peaks: 1160 INFO @ Sun, 21 Jun 2020 17:50:44: start model_add_line... INFO @ Sun, 21 Jun 2020 17:50:44: start X-correlation... INFO @ Sun, 21 Jun 2020 17:50:44: end of X-cor INFO @ Sun, 21 Jun 2020 17:50:44: #2 finished! INFO @ Sun, 21 Jun 2020 17:50:44: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 17:50:44: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 17:50:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.10_model.r INFO @ Sun, 21 Jun 2020 17:50:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:50:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:50:47: 3000000 INFO @ Sun, 21 Jun 2020 17:50:52: 4000000 INFO @ Sun, 21 Jun 2020 17:50:57: 5000000 INFO @ Sun, 21 Jun 2020 17:50:59: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:51:03: 6000000 INFO @ Sun, 21 Jun 2020 17:51:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:51:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:51:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.10_summits.bed INFO @ Sun, 21 Jun 2020 17:51:07: Done! pass1 - making usageList (573 chroms): 1 millis pass2 - checking and writing primary data (1221 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:51:08: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:51:10: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 17:51:10: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 17:51:10: #1 total tags in treatment: 7256732 INFO @ Sun, 21 Jun 2020 17:51:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:51:10: #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 17:51:10: #1 tags after filtering in treatment: 7256730 INFO @ Sun, 21 Jun 2020 17:51:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:51:10: #1 finished! INFO @ Sun, 21 Jun 2020 17:51:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:51:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:51:11: #2 number of paired peaks: 1160 INFO @ Sun, 21 Jun 2020 17:51:11: start model_add_line... INFO @ Sun, 21 Jun 2020 17:51:11: start X-correlation... INFO @ Sun, 21 Jun 2020 17:51:11: end of X-cor INFO @ Sun, 21 Jun 2020 17:51:11: #2 finished! INFO @ Sun, 21 Jun 2020 17:51:11: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 17:51:11: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 17:51:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.20_model.r INFO @ Sun, 21 Jun 2020 17:51:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:51:11: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:51:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:51:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:51:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:51:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1537617/SRX1537617.20_summits.bed INFO @ Sun, 21 Jun 2020 17:51:34: Done! pass1 - making usageList (471 chroms): 1 millis pass2 - checking and writing primary data (1020 records, 4 fields): 13 millis CompletedMACS2peakCalling