Job ID = 5720692 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,333,096 reads read : 13,333,096 reads written : 13,333,096 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR7148577.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: 00:03:00 13333096 reads; of these: 13333096 (100.00%) were unpaired; of these: 557797 (4.18%) aligned 0 times 11452616 (85.90%) aligned exactly 1 time 1322683 (9.92%) aligned >1 times 95.82% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 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 8 files... [bam_rmdupse_core] 1170668 / 12775299 = 0.0916 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 01:01:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.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 01:01:20: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:01:20: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:01:26: 1000000 INFO @ Thu, 16 Apr 2020 01:01:32: 2000000 INFO @ Thu, 16 Apr 2020 01:01:37: 3000000 INFO @ Thu, 16 Apr 2020 01:01:43: 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 @ Thu, 16 Apr 2020 01:01:49: 5000000 INFO @ Thu, 16 Apr 2020 01:01:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.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 01:01:49: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:01:49: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:01:55: 6000000 INFO @ Thu, 16 Apr 2020 01:01:56: 1000000 INFO @ Thu, 16 Apr 2020 01:02:02: 7000000 INFO @ Thu, 16 Apr 2020 01:02:02: 2000000 INFO @ Thu, 16 Apr 2020 01:02:08: 8000000 INFO @ Thu, 16 Apr 2020 01:02:09: 3000000 INFO @ Thu, 16 Apr 2020 01:02:15: 9000000 INFO @ Thu, 16 Apr 2020 01:02:15: 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 01:02:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.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 01:02:20: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:02:20: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:02:21: 10000000 INFO @ Thu, 16 Apr 2020 01:02:22: 5000000 INFO @ Thu, 16 Apr 2020 01:02:27: 1000000 INFO @ Thu, 16 Apr 2020 01:02:28: 11000000 INFO @ Thu, 16 Apr 2020 01:02:28: 6000000 INFO @ Thu, 16 Apr 2020 01:02:32: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 01:02:32: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 01:02:32: #1 total tags in treatment: 11604631 INFO @ Thu, 16 Apr 2020 01:02:32: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:02:32: #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 01:02:32: #1 tags after filtering in treatment: 11604631 INFO @ Thu, 16 Apr 2020 01:02:32: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:02:32: #1 finished! INFO @ Thu, 16 Apr 2020 01:02:32: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:02:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:02:33: #2 number of paired peaks: 347 WARNING @ Thu, 16 Apr 2020 01:02:33: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Thu, 16 Apr 2020 01:02:33: start model_add_line... INFO @ Thu, 16 Apr 2020 01:02:33: start X-correlation... INFO @ Thu, 16 Apr 2020 01:02:33: end of X-cor INFO @ Thu, 16 Apr 2020 01:02:33: #2 finished! INFO @ Thu, 16 Apr 2020 01:02:33: #2 predicted fragment length is 140 bps INFO @ Thu, 16 Apr 2020 01:02:33: #2 alternative fragment length(s) may be 140 bps INFO @ Thu, 16 Apr 2020 01:02:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.05_model.r INFO @ Thu, 16 Apr 2020 01:02:33: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:02:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:02:33: 2000000 INFO @ Thu, 16 Apr 2020 01:02:35: 7000000 INFO @ Thu, 16 Apr 2020 01:02:40: 3000000 INFO @ Thu, 16 Apr 2020 01:02:41: 8000000 INFO @ Thu, 16 Apr 2020 01:02:47: 4000000 INFO @ Thu, 16 Apr 2020 01:02:48: 9000000 INFO @ Thu, 16 Apr 2020 01:02:53: 5000000 INFO @ Thu, 16 Apr 2020 01:02:54: 10000000 INFO @ Thu, 16 Apr 2020 01:02:55: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:03:00: 6000000 INFO @ Thu, 16 Apr 2020 01:03:01: 11000000 INFO @ Thu, 16 Apr 2020 01:03:05: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 01:03:05: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 01:03:05: #1 total tags in treatment: 11604631 INFO @ Thu, 16 Apr 2020 01:03:05: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:03:05: #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 01:03:05: #1 tags after filtering in treatment: 11604631 INFO @ Thu, 16 Apr 2020 01:03:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:03:05: #1 finished! INFO @ Thu, 16 Apr 2020 01:03:05: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:03:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:03:05: #2 number of paired peaks: 347 WARNING @ Thu, 16 Apr 2020 01:03:05: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Thu, 16 Apr 2020 01:03:05: start model_add_line... INFO @ Thu, 16 Apr 2020 01:03:06: start X-correlation... INFO @ Thu, 16 Apr 2020 01:03:06: end of X-cor INFO @ Thu, 16 Apr 2020 01:03:06: #2 finished! INFO @ Thu, 16 Apr 2020 01:03:06: #2 predicted fragment length is 140 bps INFO @ Thu, 16 Apr 2020 01:03:06: #2 alternative fragment length(s) may be 140 bps INFO @ Thu, 16 Apr 2020 01:03:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.10_model.r INFO @ Thu, 16 Apr 2020 01:03:06: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:03:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:03:06: 7000000 INFO @ Thu, 16 Apr 2020 01:03:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:03:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:03:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.05_summits.bed INFO @ Thu, 16 Apr 2020 01:03:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (9606 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:03:12: 8000000 INFO @ Thu, 16 Apr 2020 01:03:18: 9000000 INFO @ Thu, 16 Apr 2020 01:03:24: 10000000 INFO @ Thu, 16 Apr 2020 01:03:29: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:03:30: 11000000 INFO @ Thu, 16 Apr 2020 01:03:34: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 01:03:34: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 01:03:34: #1 total tags in treatment: 11604631 INFO @ Thu, 16 Apr 2020 01:03:34: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:03:34: #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 01:03:34: #1 tags after filtering in treatment: 11604631 INFO @ Thu, 16 Apr 2020 01:03:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:03:34: #1 finished! INFO @ Thu, 16 Apr 2020 01:03:34: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:03:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:03:35: #2 number of paired peaks: 347 WARNING @ Thu, 16 Apr 2020 01:03:35: Fewer paired peaks (347) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 347 pairs to build model! INFO @ Thu, 16 Apr 2020 01:03:35: start model_add_line... INFO @ Thu, 16 Apr 2020 01:03:35: start X-correlation... INFO @ Thu, 16 Apr 2020 01:03:35: end of X-cor INFO @ Thu, 16 Apr 2020 01:03:35: #2 finished! INFO @ Thu, 16 Apr 2020 01:03:35: #2 predicted fragment length is 140 bps INFO @ Thu, 16 Apr 2020 01:03:35: #2 alternative fragment length(s) may be 140 bps INFO @ Thu, 16 Apr 2020 01:03:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.20_model.r INFO @ Thu, 16 Apr 2020 01:03:35: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:03:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:03:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:03:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:03:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.10_summits.bed INFO @ Thu, 16 Apr 2020 01:03:41: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (3472 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:03:58: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:04:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:04:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:04:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4068066/SRX4068066.20_summits.bed INFO @ Thu, 16 Apr 2020 01:04:10: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (429 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。