Job ID = 6627368 SRX = SRX8521292 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:00:01 Multiseed full-index search: 00:07:29 54985481 reads; of these: 54985481 (100.00%) were unpaired; of these: 46891226 (85.28%) aligned 0 times 6206241 (11.29%) aligned exactly 1 time 1888014 (3.43%) aligned >1 times 14.72% overall alignment rate Time searching: 00:07:30 Overall time: 00:07:30 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_rmdupse_core] 1300128 / 8094255 = 0.1606 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 @ Tue, 14 Jul 2020 11:21:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.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 @ Tue, 14 Jul 2020 11:21:47: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:21:47: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:21:52: 1000000 INFO @ Tue, 14 Jul 2020 11:21:58: 2000000 INFO @ Tue, 14 Jul 2020 11:22:03: 3000000 INFO @ Tue, 14 Jul 2020 11:22:09: 4000000 INFO @ Tue, 14 Jul 2020 11:22:14: 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 @ Tue, 14 Jul 2020 11:22:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.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 @ Tue, 14 Jul 2020 11:22:17: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:22:17: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:22:21: 6000000 INFO @ Tue, 14 Jul 2020 11:22:24: 1000000 INFO @ Tue, 14 Jul 2020 11:22:26: #1 tag size is determined as 64 bps INFO @ Tue, 14 Jul 2020 11:22:26: #1 tag size = 64 INFO @ Tue, 14 Jul 2020 11:22:26: #1 total tags in treatment: 6794127 INFO @ Tue, 14 Jul 2020 11:22:26: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:22:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:22:26: #1 tags after filtering in treatment: 6793953 INFO @ Tue, 14 Jul 2020 11:22:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:22:26: #1 finished! INFO @ Tue, 14 Jul 2020 11:22:26: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:22:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:22:27: #2 number of paired peaks: 564 WARNING @ Tue, 14 Jul 2020 11:22:27: Fewer paired peaks (564) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 564 pairs to build model! INFO @ Tue, 14 Jul 2020 11:22:27: start model_add_line... INFO @ Tue, 14 Jul 2020 11:22:27: start X-correlation... INFO @ Tue, 14 Jul 2020 11:22:27: end of X-cor INFO @ Tue, 14 Jul 2020 11:22:27: #2 finished! INFO @ Tue, 14 Jul 2020 11:22:27: #2 predicted fragment length is 52 bps INFO @ Tue, 14 Jul 2020 11:22:27: #2 alternative fragment length(s) may be 4,52 bps INFO @ Tue, 14 Jul 2020 11:22:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.05_model.r WARNING @ Tue, 14 Jul 2020 11:22:27: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:22:27: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Tue, 14 Jul 2020 11:22:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:22:27: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:22:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:22:30: 2000000 INFO @ Tue, 14 Jul 2020 11:22:36: 3000000 INFO @ Tue, 14 Jul 2020 11:22:41: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:22:43: 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 @ Tue, 14 Jul 2020 11:22:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.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 @ Tue, 14 Jul 2020 11:22:47: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:22:47: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:22:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:22:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:22:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.05_summits.bed INFO @ Tue, 14 Jul 2020 11:22:47: Done! pass1 - making usageList (186 chroms): 1 millis pass2 - checking and writing primary data (1289 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:22:50: 5000000 INFO @ Tue, 14 Jul 2020 11:22:54: 1000000 INFO @ Tue, 14 Jul 2020 11:22:58: 6000000 INFO @ Tue, 14 Jul 2020 11:23:01: 2000000 INFO @ Tue, 14 Jul 2020 11:23:04: #1 tag size is determined as 64 bps INFO @ Tue, 14 Jul 2020 11:23:04: #1 tag size = 64 INFO @ Tue, 14 Jul 2020 11:23:04: #1 total tags in treatment: 6794127 INFO @ Tue, 14 Jul 2020 11:23:04: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:23:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:23:04: #1 tags after filtering in treatment: 6793953 INFO @ Tue, 14 Jul 2020 11:23:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:23:04: #1 finished! INFO @ Tue, 14 Jul 2020 11:23:04: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:23:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:23:04: #2 number of paired peaks: 564 WARNING @ Tue, 14 Jul 2020 11:23:04: Fewer paired peaks (564) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 564 pairs to build model! INFO @ Tue, 14 Jul 2020 11:23:04: start model_add_line... INFO @ Tue, 14 Jul 2020 11:23:04: start X-correlation... INFO @ Tue, 14 Jul 2020 11:23:04: end of X-cor INFO @ Tue, 14 Jul 2020 11:23:04: #2 finished! INFO @ Tue, 14 Jul 2020 11:23:04: #2 predicted fragment length is 52 bps INFO @ Tue, 14 Jul 2020 11:23:04: #2 alternative fragment length(s) may be 4,52 bps INFO @ Tue, 14 Jul 2020 11:23:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.10_model.r WARNING @ Tue, 14 Jul 2020 11:23:05: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:23:05: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Tue, 14 Jul 2020 11:23:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:23:05: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:23:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:23:08: 3000000 INFO @ Tue, 14 Jul 2020 11:23:15: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:23:19: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:23:22: 5000000 INFO @ Tue, 14 Jul 2020 11:23:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:23:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:23:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.10_summits.bed INFO @ Tue, 14 Jul 2020 11:23:26: Done! pass1 - making usageList (124 chroms): 1 millis pass2 - checking and writing primary data (439 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:23:29: 6000000 INFO @ Tue, 14 Jul 2020 11:23:34: #1 tag size is determined as 64 bps INFO @ Tue, 14 Jul 2020 11:23:34: #1 tag size = 64 INFO @ Tue, 14 Jul 2020 11:23:34: #1 total tags in treatment: 6794127 INFO @ Tue, 14 Jul 2020 11:23:34: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:23:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:23:35: #1 tags after filtering in treatment: 6793953 INFO @ Tue, 14 Jul 2020 11:23:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:23:35: #1 finished! INFO @ Tue, 14 Jul 2020 11:23:35: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:23:35: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:23:35: #2 number of paired peaks: 564 WARNING @ Tue, 14 Jul 2020 11:23:35: Fewer paired peaks (564) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 564 pairs to build model! INFO @ Tue, 14 Jul 2020 11:23:35: start model_add_line... INFO @ Tue, 14 Jul 2020 11:23:35: start X-correlation... INFO @ Tue, 14 Jul 2020 11:23:35: end of X-cor INFO @ Tue, 14 Jul 2020 11:23:35: #2 finished! INFO @ Tue, 14 Jul 2020 11:23:35: #2 predicted fragment length is 52 bps INFO @ Tue, 14 Jul 2020 11:23:35: #2 alternative fragment length(s) may be 4,52 bps INFO @ Tue, 14 Jul 2020 11:23:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.20_model.r WARNING @ Tue, 14 Jul 2020 11:23:35: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:23:35: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Tue, 14 Jul 2020 11:23:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:23:35: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:23:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:23:49: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:23:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:23:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:23:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521292/SRX8521292.20_summits.bed INFO @ Tue, 14 Jul 2020 11:23:56: Done! pass1 - making usageList (71 chroms): 1 millis pass2 - checking and writing primary data (128 records, 4 fields): 4 millis CompletedMACS2peakCalling