Job ID = 5720593 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,009,981 reads read : 13,009,981 reads written : 13,009,981 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289721.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: 00:04:01 13009981 reads; of these: 13009981 (100.00%) were unpaired; of these: 1621302 (12.46%) aligned 0 times 7694077 (59.14%) aligned exactly 1 time 3694602 (28.40%) aligned >1 times 87.54% overall alignment rate Time searching: 00:04:01 Overall time: 00:04:01 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] 2013380 / 11388679 = 0.1768 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 00:48:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.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 00:48:58: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:48:58: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:49:04: 1000000 INFO @ Thu, 16 Apr 2020 00:49:10: 2000000 INFO @ Thu, 16 Apr 2020 00:49:15: 3000000 INFO @ Thu, 16 Apr 2020 00:49:21: 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 00:49:26: 5000000 INFO @ Thu, 16 Apr 2020 00:49:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.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 00:49:28: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:49:28: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:49:32: 6000000 INFO @ Thu, 16 Apr 2020 00:49:34: 1000000 INFO @ Thu, 16 Apr 2020 00:49:38: 7000000 INFO @ Thu, 16 Apr 2020 00:49:39: 2000000 INFO @ Thu, 16 Apr 2020 00:49:43: 8000000 INFO @ Thu, 16 Apr 2020 00:49:45: 3000000 INFO @ Thu, 16 Apr 2020 00:49:49: 9000000 INFO @ Thu, 16 Apr 2020 00:49:51: 4000000 INFO @ Thu, 16 Apr 2020 00:49:51: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:49:51: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:49:51: #1 total tags in treatment: 9375299 INFO @ Thu, 16 Apr 2020 00:49:51: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:49:51: #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 00:49:51: #1 tags after filtering in treatment: 9375299 INFO @ Thu, 16 Apr 2020 00:49:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:49:51: #1 finished! INFO @ Thu, 16 Apr 2020 00:49:51: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:49:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:49:52: #2 number of paired peaks: 647 WARNING @ Thu, 16 Apr 2020 00:49:52: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Thu, 16 Apr 2020 00:49:52: start model_add_line... INFO @ Thu, 16 Apr 2020 00:49:52: start X-correlation... INFO @ Thu, 16 Apr 2020 00:49:52: end of X-cor INFO @ Thu, 16 Apr 2020 00:49:52: #2 finished! INFO @ Thu, 16 Apr 2020 00:49:52: #2 predicted fragment length is 51 bps INFO @ Thu, 16 Apr 2020 00:49:52: #2 alternative fragment length(s) may be 51 bps INFO @ Thu, 16 Apr 2020 00:49:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.05_model.r WARNING @ Thu, 16 Apr 2020 00:49:52: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:49:52: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Thu, 16 Apr 2020 00:49:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:49:52: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:49:52: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... INFO @ Thu, 16 Apr 2020 00:49:56: 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 @ Thu, 16 Apr 2020 00:49:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.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 00:49:58: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:49:58: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:50:02: 6000000 INFO @ Thu, 16 Apr 2020 00:50:03: 1000000 INFO @ Thu, 16 Apr 2020 00:50:07: 7000000 INFO @ Thu, 16 Apr 2020 00:50:09: 2000000 INFO @ Thu, 16 Apr 2020 00:50:10: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:50:13: 8000000 INFO @ Thu, 16 Apr 2020 00:50:14: 3000000 INFO @ Thu, 16 Apr 2020 00:50:18: 9000000 INFO @ Thu, 16 Apr 2020 00:50:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:50:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:50:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.05_summits.bed INFO @ Thu, 16 Apr 2020 00:50:19: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1812 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:50:20: 4000000 INFO @ Thu, 16 Apr 2020 00:50:20: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:50:20: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:50:20: #1 total tags in treatment: 9375299 INFO @ Thu, 16 Apr 2020 00:50:20: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:50:20: #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 00:50:20: #1 tags after filtering in treatment: 9375299 INFO @ Thu, 16 Apr 2020 00:50:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:50:20: #1 finished! INFO @ Thu, 16 Apr 2020 00:50:20: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:50:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:50:21: #2 number of paired peaks: 647 WARNING @ Thu, 16 Apr 2020 00:50:21: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Thu, 16 Apr 2020 00:50:21: start model_add_line... INFO @ Thu, 16 Apr 2020 00:50:21: start X-correlation... INFO @ Thu, 16 Apr 2020 00:50:21: end of X-cor INFO @ Thu, 16 Apr 2020 00:50:21: #2 finished! INFO @ Thu, 16 Apr 2020 00:50:21: #2 predicted fragment length is 51 bps INFO @ Thu, 16 Apr 2020 00:50:21: #2 alternative fragment length(s) may be 51 bps INFO @ Thu, 16 Apr 2020 00:50:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.10_model.r WARNING @ Thu, 16 Apr 2020 00:50:21: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:50:21: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Thu, 16 Apr 2020 00:50:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:50:21: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:50:21: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:50:25: 5000000 INFO @ Thu, 16 Apr 2020 00:50:31: 6000000 INFO @ Thu, 16 Apr 2020 00:50:36: 7000000 INFO @ Thu, 16 Apr 2020 00:50:40: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:50:41: 8000000 INFO @ Thu, 16 Apr 2020 00:50:47: 9000000 INFO @ Thu, 16 Apr 2020 00:50:49: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 00:50:49: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 00:50:49: #1 total tags in treatment: 9375299 INFO @ Thu, 16 Apr 2020 00:50:49: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:50:49: #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 00:50:49: #1 tags after filtering in treatment: 9375299 INFO @ Thu, 16 Apr 2020 00:50:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:50:49: #1 finished! INFO @ Thu, 16 Apr 2020 00:50:49: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:50:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:50:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:50:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:50:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.10_summits.bed INFO @ Thu, 16 Apr 2020 00:50:49: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1208 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:50:50: #2 number of paired peaks: 647 WARNING @ Thu, 16 Apr 2020 00:50:50: Fewer paired peaks (647) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 647 pairs to build model! INFO @ Thu, 16 Apr 2020 00:50:50: start model_add_line... INFO @ Thu, 16 Apr 2020 00:50:50: start X-correlation... INFO @ Thu, 16 Apr 2020 00:50:50: end of X-cor INFO @ Thu, 16 Apr 2020 00:50:50: #2 finished! INFO @ Thu, 16 Apr 2020 00:50:50: #2 predicted fragment length is 51 bps INFO @ Thu, 16 Apr 2020 00:50:50: #2 alternative fragment length(s) may be 51 bps INFO @ Thu, 16 Apr 2020 00:50:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.20_model.r WARNING @ Thu, 16 Apr 2020 00:50:50: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:50:50: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Thu, 16 Apr 2020 00:50:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:50:50: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:50:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:51:08: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:51:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:51:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:51:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592444/SRX2592444.20_summits.bed INFO @ Thu, 16 Apr 2020 00:51:18: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (917 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。