Job ID = 5720440 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,616,546 reads read : 22,616,546 reads written : 22,616,546 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289686.sra.cache’: No such file or directory 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: 00:07:00 22616546 reads; of these: 22616546 (100.00%) were unpaired; of these: 1672167 (7.39%) aligned 0 times 16394075 (72.49%) aligned exactly 1 time 4550304 (20.12%) aligned >1 times 92.61% overall alignment rate Time searching: 00:07:00 Overall time: 00:07:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 5649439 / 20944379 = 0.2697 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 @ Thu, 16 Apr 2020 00:39:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.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 @ Thu, 16 Apr 2020 00:39:25: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:39:25: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:39:30: 1000000 INFO @ Thu, 16 Apr 2020 00:39:36: 2000000 INFO @ Thu, 16 Apr 2020 00:39:41: 3000000 INFO @ Thu, 16 Apr 2020 00:39:47: 4000000 INFO @ Thu, 16 Apr 2020 00:39:52: 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 @ Thu, 16 Apr 2020 00:39:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.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 @ Thu, 16 Apr 2020 00:39:55: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:39:55: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:39:58: 6000000 INFO @ Thu, 16 Apr 2020 00:40:02: 1000000 INFO @ Thu, 16 Apr 2020 00:40:05: 7000000 INFO @ Thu, 16 Apr 2020 00:40:09: 2000000 INFO @ Thu, 16 Apr 2020 00:40:11: 8000000 INFO @ Thu, 16 Apr 2020 00:40:16: 3000000 INFO @ Thu, 16 Apr 2020 00:40:17: 9000000 INFO @ Thu, 16 Apr 2020 00:40:23: 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 @ Thu, 16 Apr 2020 00:40:23: 10000000 INFO @ Thu, 16 Apr 2020 00:40:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.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 @ Thu, 16 Apr 2020 00:40:25: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:40:25: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:40:30: 5000000 INFO @ Thu, 16 Apr 2020 00:40:30: 11000000 INFO @ Thu, 16 Apr 2020 00:40:32: 1000000 INFO @ Thu, 16 Apr 2020 00:40:36: 12000000 INFO @ Thu, 16 Apr 2020 00:40:37: 6000000 INFO @ Thu, 16 Apr 2020 00:40:39: 2000000 INFO @ Thu, 16 Apr 2020 00:40:43: 13000000 INFO @ Thu, 16 Apr 2020 00:40:44: 7000000 INFO @ Thu, 16 Apr 2020 00:40:46: 3000000 INFO @ Thu, 16 Apr 2020 00:40:50: 14000000 INFO @ Thu, 16 Apr 2020 00:40:51: 8000000 INFO @ Thu, 16 Apr 2020 00:40:53: 4000000 INFO @ Thu, 16 Apr 2020 00:40:56: 15000000 INFO @ Thu, 16 Apr 2020 00:40:58: 9000000 INFO @ Thu, 16 Apr 2020 00:40:58: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:40:58: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:40:58: #1 total tags in treatment: 15294940 INFO @ Thu, 16 Apr 2020 00:40:58: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:40:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:40:59: #1 tags after filtering in treatment: 15294940 INFO @ Thu, 16 Apr 2020 00:40:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:40:59: #1 finished! INFO @ Thu, 16 Apr 2020 00:40:59: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:40:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:40:59: 5000000 INFO @ Thu, 16 Apr 2020 00:41:00: #2 number of paired peaks: 540 WARNING @ Thu, 16 Apr 2020 00:41:00: Fewer paired peaks (540) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 540 pairs to build model! INFO @ Thu, 16 Apr 2020 00:41:00: start model_add_line... INFO @ Thu, 16 Apr 2020 00:41:00: start X-correlation... INFO @ Thu, 16 Apr 2020 00:41:00: end of X-cor INFO @ Thu, 16 Apr 2020 00:41:00: #2 finished! INFO @ Thu, 16 Apr 2020 00:41:00: #2 predicted fragment length is 200 bps INFO @ Thu, 16 Apr 2020 00:41:00: #2 alternative fragment length(s) may be 4,200 bps INFO @ Thu, 16 Apr 2020 00:41:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.05_model.r INFO @ Thu, 16 Apr 2020 00:41:00: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:41:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:41:05: 10000000 INFO @ Thu, 16 Apr 2020 00:41:06: 6000000 INFO @ Thu, 16 Apr 2020 00:41:11: 11000000 INFO @ Thu, 16 Apr 2020 00:41:13: 7000000 INFO @ Thu, 16 Apr 2020 00:41:18: 12000000 INFO @ Thu, 16 Apr 2020 00:41:19: 8000000 INFO @ Thu, 16 Apr 2020 00:41:25: 13000000 INFO @ Thu, 16 Apr 2020 00:41:26: 9000000 INFO @ Thu, 16 Apr 2020 00:41:32: 14000000 INFO @ Thu, 16 Apr 2020 00:41:32: 10000000 INFO @ Thu, 16 Apr 2020 00:41:38: 15000000 INFO @ Thu, 16 Apr 2020 00:41:39: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:41:39: 11000000 INFO @ Thu, 16 Apr 2020 00:41:41: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:41:41: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:41:41: #1 total tags in treatment: 15294940 INFO @ Thu, 16 Apr 2020 00:41:41: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:41:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:41:41: #1 tags after filtering in treatment: 15294940 INFO @ Thu, 16 Apr 2020 00:41:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:41:41: #1 finished! INFO @ Thu, 16 Apr 2020 00:41:41: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:41:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:41:42: #2 number of paired peaks: 540 WARNING @ Thu, 16 Apr 2020 00:41:42: Fewer paired peaks (540) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 540 pairs to build model! INFO @ Thu, 16 Apr 2020 00:41:42: start model_add_line... INFO @ Thu, 16 Apr 2020 00:41:42: start X-correlation... INFO @ Thu, 16 Apr 2020 00:41:42: end of X-cor INFO @ Thu, 16 Apr 2020 00:41:42: #2 finished! INFO @ Thu, 16 Apr 2020 00:41:42: #2 predicted fragment length is 200 bps INFO @ Thu, 16 Apr 2020 00:41:42: #2 alternative fragment length(s) may be 4,200 bps INFO @ Thu, 16 Apr 2020 00:41:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.10_model.r INFO @ Thu, 16 Apr 2020 00:41:42: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:41:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:41:45: 12000000 INFO @ Thu, 16 Apr 2020 00:41:51: 13000000 INFO @ Thu, 16 Apr 2020 00:41:58: 14000000 INFO @ Thu, 16 Apr 2020 00:41:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:41:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:41:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.05_summits.bed INFO @ Thu, 16 Apr 2020 00:41:59: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (15298 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:42:04: 15000000 INFO @ Thu, 16 Apr 2020 00:42:06: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:42:06: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:42:06: #1 total tags in treatment: 15294940 INFO @ Thu, 16 Apr 2020 00:42:06: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:42:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:42:06: #1 tags after filtering in treatment: 15294940 INFO @ Thu, 16 Apr 2020 00:42:06: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:42:06: #1 finished! INFO @ Thu, 16 Apr 2020 00:42:06: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:42:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:42:07: #2 number of paired peaks: 540 WARNING @ Thu, 16 Apr 2020 00:42:07: Fewer paired peaks (540) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 540 pairs to build model! INFO @ Thu, 16 Apr 2020 00:42:07: start model_add_line... INFO @ Thu, 16 Apr 2020 00:42:07: start X-correlation... INFO @ Thu, 16 Apr 2020 00:42:07: end of X-cor INFO @ Thu, 16 Apr 2020 00:42:07: #2 finished! INFO @ Thu, 16 Apr 2020 00:42:07: #2 predicted fragment length is 200 bps INFO @ Thu, 16 Apr 2020 00:42:07: #2 alternative fragment length(s) may be 4,200 bps INFO @ Thu, 16 Apr 2020 00:42:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.20_model.r INFO @ Thu, 16 Apr 2020 00:42:07: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:42:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:42:20: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:42:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:42:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:42:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.10_summits.bed INFO @ Thu, 16 Apr 2020 00:42:39: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (9635 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:42:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:42:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:42:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:42:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592409/SRX2592409.20_summits.bed INFO @ Thu, 16 Apr 2020 00:42:59: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4670 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。