Job ID = 5720710 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,945,583 reads read : 15,945,583 reads written : 15,945,583 rm: cannot remove ‘[DSE]RR*’: 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: 00:03:55 15945583 reads; of these: 15945583 (100.00%) were unpaired; of these: 1613240 (10.12%) aligned 0 times 11495118 (72.09%) aligned exactly 1 time 2837225 (17.79%) aligned >1 times 89.88% overall alignment rate Time searching: 00:03:55 Overall time: 00:03:55 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] 1580463 / 14332343 = 0.1103 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 01:15:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.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 01:15:56: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:15:56: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:16:03: 1000000 INFO @ Thu, 16 Apr 2020 01:16:10: 2000000 INFO @ Thu, 16 Apr 2020 01:16:17: 3000000 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 01:16:25: 4000000 INFO @ Thu, 16 Apr 2020 01:16:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.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 01:16:26: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:16:26: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:16:31: 5000000 INFO @ Thu, 16 Apr 2020 01:16:34: 1000000 INFO @ Thu, 16 Apr 2020 01:16:38: 6000000 INFO @ Thu, 16 Apr 2020 01:16:41: 2000000 INFO @ Thu, 16 Apr 2020 01:16:45: 7000000 INFO @ Thu, 16 Apr 2020 01:16:49: 3000000 INFO @ Thu, 16 Apr 2020 01:16:51: 8000000 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 01:16:56: 4000000 INFO @ Thu, 16 Apr 2020 01:16:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.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 01:16:56: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:16:56: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:16:58: 9000000 INFO @ Thu, 16 Apr 2020 01:17:03: 5000000 INFO @ Thu, 16 Apr 2020 01:17:04: 1000000 INFO @ Thu, 16 Apr 2020 01:17:06: 10000000 INFO @ Thu, 16 Apr 2020 01:17:11: 6000000 INFO @ Thu, 16 Apr 2020 01:17:12: 2000000 INFO @ Thu, 16 Apr 2020 01:17:16: 11000000 INFO @ Thu, 16 Apr 2020 01:17:18: 7000000 INFO @ Thu, 16 Apr 2020 01:17:19: 3000000 INFO @ Thu, 16 Apr 2020 01:17:25: 12000000 INFO @ Thu, 16 Apr 2020 01:17:26: 8000000 INFO @ Thu, 16 Apr 2020 01:17:27: 4000000 INFO @ Thu, 16 Apr 2020 01:17:31: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:17:31: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:17:31: #1 total tags in treatment: 12751880 INFO @ Thu, 16 Apr 2020 01:17:31: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:17:31: #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 01:17:31: #1 tags after filtering in treatment: 12751880 INFO @ Thu, 16 Apr 2020 01:17:31: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:17:31: #1 finished! INFO @ Thu, 16 Apr 2020 01:17:31: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:17:31: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:17:32: #2 number of paired peaks: 118 WARNING @ Thu, 16 Apr 2020 01:17:32: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Thu, 16 Apr 2020 01:17:32: start model_add_line... INFO @ Thu, 16 Apr 2020 01:17:32: start X-correlation... INFO @ Thu, 16 Apr 2020 01:17:32: end of X-cor INFO @ Thu, 16 Apr 2020 01:17:32: #2 finished! INFO @ Thu, 16 Apr 2020 01:17:32: #2 predicted fragment length is 47 bps INFO @ Thu, 16 Apr 2020 01:17:32: #2 alternative fragment length(s) may be 1,47,95,98,111,126,177,186,189,204,274,287,457,573,591 bps INFO @ Thu, 16 Apr 2020 01:17:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.05_model.r WARNING @ Thu, 16 Apr 2020 01:17:32: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:17:32: #2 You may need to consider one of the other alternative d(s): 1,47,95,98,111,126,177,186,189,204,274,287,457,573,591 WARNING @ Thu, 16 Apr 2020 01:17:32: #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 01:17:32: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:17:32: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:17:33: 9000000 INFO @ Thu, 16 Apr 2020 01:17:34: 5000000 INFO @ Thu, 16 Apr 2020 01:17:41: 10000000 INFO @ Thu, 16 Apr 2020 01:17:41: 6000000 INFO @ Thu, 16 Apr 2020 01:17:48: 11000000 INFO @ Thu, 16 Apr 2020 01:17:49: 7000000 INFO @ Thu, 16 Apr 2020 01:17:55: 12000000 INFO @ Thu, 16 Apr 2020 01:17:56: 8000000 INFO @ Thu, 16 Apr 2020 01:17:57: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:18:01: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:18:01: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:18:01: #1 total tags in treatment: 12751880 INFO @ Thu, 16 Apr 2020 01:18:01: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:18:01: #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 01:18:01: #1 tags after filtering in treatment: 12751880 INFO @ Thu, 16 Apr 2020 01:18:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:18:01: #1 finished! INFO @ Thu, 16 Apr 2020 01:18:01: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:18:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:18:02: #2 number of paired peaks: 118 WARNING @ Thu, 16 Apr 2020 01:18:02: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Thu, 16 Apr 2020 01:18:02: start model_add_line... INFO @ Thu, 16 Apr 2020 01:18:02: start X-correlation... INFO @ Thu, 16 Apr 2020 01:18:02: end of X-cor INFO @ Thu, 16 Apr 2020 01:18:02: #2 finished! INFO @ Thu, 16 Apr 2020 01:18:02: #2 predicted fragment length is 47 bps INFO @ Thu, 16 Apr 2020 01:18:02: #2 alternative fragment length(s) may be 1,47,95,98,111,126,177,186,189,204,274,287,457,573,591 bps INFO @ Thu, 16 Apr 2020 01:18:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.10_model.r WARNING @ Thu, 16 Apr 2020 01:18:02: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:18:02: #2 You may need to consider one of the other alternative d(s): 1,47,95,98,111,126,177,186,189,204,274,287,457,573,591 WARNING @ Thu, 16 Apr 2020 01:18:02: #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 01:18:02: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:18:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:18:03: 9000000 INFO @ Thu, 16 Apr 2020 01:18:10: 10000000 INFO @ Thu, 16 Apr 2020 01:18:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:18:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:18:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.05_summits.bed INFO @ Thu, 16 Apr 2020 01:18:11: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (341 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:18:17: 11000000 INFO @ Thu, 16 Apr 2020 01:18:24: 12000000 INFO @ Thu, 16 Apr 2020 01:18:27: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:18:29: #1 tag size is determined as 49 bps INFO @ Thu, 16 Apr 2020 01:18:29: #1 tag size = 49 INFO @ Thu, 16 Apr 2020 01:18:29: #1 total tags in treatment: 12751880 INFO @ Thu, 16 Apr 2020 01:18:29: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:18:29: #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 01:18:29: #1 tags after filtering in treatment: 12751880 INFO @ Thu, 16 Apr 2020 01:18:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:18:29: #1 finished! INFO @ Thu, 16 Apr 2020 01:18:29: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:18:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:18:30: #2 number of paired peaks: 118 WARNING @ Thu, 16 Apr 2020 01:18:30: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Thu, 16 Apr 2020 01:18:30: start model_add_line... INFO @ Thu, 16 Apr 2020 01:18:30: start X-correlation... INFO @ Thu, 16 Apr 2020 01:18:30: end of X-cor INFO @ Thu, 16 Apr 2020 01:18:30: #2 finished! INFO @ Thu, 16 Apr 2020 01:18:30: #2 predicted fragment length is 47 bps INFO @ Thu, 16 Apr 2020 01:18:30: #2 alternative fragment length(s) may be 1,47,95,98,111,126,177,186,189,204,274,287,457,573,591 bps INFO @ Thu, 16 Apr 2020 01:18:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.20_model.r WARNING @ Thu, 16 Apr 2020 01:18:30: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:18:30: #2 You may need to consider one of the other alternative d(s): 1,47,95,98,111,126,177,186,189,204,274,287,457,573,591 WARNING @ Thu, 16 Apr 2020 01:18:30: #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 01:18:30: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:18:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:18:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:18:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:18:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.10_summits.bed INFO @ Thu, 16 Apr 2020 01:18:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (140 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:18:54: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:19:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:19:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:19:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4158174/SRX4158174.20_summits.bed INFO @ Thu, 16 Apr 2020 01:19:06: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (54 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。