Job ID = 14167752 SRX = SRX6407575 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: 00:00:00 Multiseed full-index search: 00:03:24 8196249 reads; of these: 8196249 (100.00%) were unpaired; of these: 402108 (4.91%) aligned 0 times 6865581 (83.76%) aligned exactly 1 time 928560 (11.33%) aligned >1 times 95.09% overall alignment rate Time searching: 00:03:24 Overall time: 00:03:24 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] 477786 / 7794141 = 0.0613 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 13:24:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.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 @ Fri, 10 Dec 2021 13:24:44: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:24:44: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:24:51: 1000000 INFO @ Fri, 10 Dec 2021 13:24:57: 2000000 INFO @ Fri, 10 Dec 2021 13:25:03: 3000000 INFO @ Fri, 10 Dec 2021 13:25:09: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 13:25:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.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 @ Fri, 10 Dec 2021 13:25:15: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:25:15: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:25:15: 5000000 INFO @ Fri, 10 Dec 2021 13:25:21: 1000000 INFO @ Fri, 10 Dec 2021 13:25:22: 6000000 INFO @ Fri, 10 Dec 2021 13:25:28: 2000000 INFO @ Fri, 10 Dec 2021 13:25:28: 7000000 INFO @ Fri, 10 Dec 2021 13:25:31: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 13:25:31: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 13:25:31: #1 total tags in treatment: 7316355 INFO @ Fri, 10 Dec 2021 13:25:31: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:25:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:25:31: #1 tags after filtering in treatment: 7316035 INFO @ Fri, 10 Dec 2021 13:25:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:25:31: #1 finished! INFO @ Fri, 10 Dec 2021 13:25:31: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:25:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:25:32: #2 number of paired peaks: 441 WARNING @ Fri, 10 Dec 2021 13:25:32: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Fri, 10 Dec 2021 13:25:32: start model_add_line... INFO @ Fri, 10 Dec 2021 13:25:32: start X-correlation... INFO @ Fri, 10 Dec 2021 13:25:32: end of X-cor INFO @ Fri, 10 Dec 2021 13:25:32: #2 finished! INFO @ Fri, 10 Dec 2021 13:25:32: #2 predicted fragment length is 148 bps INFO @ Fri, 10 Dec 2021 13:25:32: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 10 Dec 2021 13:25:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.05_model.r WARNING @ Fri, 10 Dec 2021 13:25:32: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:25:32: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Fri, 10 Dec 2021 13:25:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:25:32: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:25:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:25:34: 3000000 INFO @ Fri, 10 Dec 2021 13:25:40: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 13:25:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.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 @ Fri, 10 Dec 2021 13:25:45: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:25:45: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:25:47: 5000000 INFO @ Fri, 10 Dec 2021 13:25:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:25:53: 1000000 INFO @ Fri, 10 Dec 2021 13:25:54: 6000000 INFO @ Fri, 10 Dec 2021 13:25:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:25:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:25:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.05_summits.bed INFO @ Fri, 10 Dec 2021 13:25:57: Done! pass1 - making usageList (205 chroms): 1 millis pass2 - checking and writing primary data (1121 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:26:00: 7000000 INFO @ Fri, 10 Dec 2021 13:26:00: 2000000 INFO @ Fri, 10 Dec 2021 13:26:02: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 13:26:02: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 13:26:02: #1 total tags in treatment: 7316355 INFO @ Fri, 10 Dec 2021 13:26:02: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:26:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:26:03: #1 tags after filtering in treatment: 7316035 INFO @ Fri, 10 Dec 2021 13:26:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:26:03: #1 finished! INFO @ Fri, 10 Dec 2021 13:26:03: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:26:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:26:03: #2 number of paired peaks: 441 WARNING @ Fri, 10 Dec 2021 13:26:03: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Fri, 10 Dec 2021 13:26:03: start model_add_line... INFO @ Fri, 10 Dec 2021 13:26:03: start X-correlation... INFO @ Fri, 10 Dec 2021 13:26:03: end of X-cor INFO @ Fri, 10 Dec 2021 13:26:03: #2 finished! INFO @ Fri, 10 Dec 2021 13:26:03: #2 predicted fragment length is 148 bps INFO @ Fri, 10 Dec 2021 13:26:03: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 10 Dec 2021 13:26:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.10_model.r WARNING @ Fri, 10 Dec 2021 13:26:03: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:26:03: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Fri, 10 Dec 2021 13:26:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:26:03: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:26:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:26:08: 3000000 INFO @ Fri, 10 Dec 2021 13:26:16: 4000000 INFO @ Fri, 10 Dec 2021 13:26:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:26:23: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:26:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:26:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:26:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.10_summits.bed INFO @ Fri, 10 Dec 2021 13:26:30: Done! pass1 - making usageList (125 chroms): 1 millis pass2 - checking and writing primary data (311 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:26:31: 6000000 INFO @ Fri, 10 Dec 2021 13:26:39: 7000000 INFO @ Fri, 10 Dec 2021 13:26:41: #1 tag size is determined as 100 bps INFO @ Fri, 10 Dec 2021 13:26:41: #1 tag size = 100 INFO @ Fri, 10 Dec 2021 13:26:41: #1 total tags in treatment: 7316355 INFO @ Fri, 10 Dec 2021 13:26:41: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:26:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 13:26:42: #1 tags after filtering in treatment: 7316035 INFO @ Fri, 10 Dec 2021 13:26:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:26:42: #1 finished! INFO @ Fri, 10 Dec 2021 13:26:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:26:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:26:42: #2 number of paired peaks: 441 WARNING @ Fri, 10 Dec 2021 13:26:42: Fewer paired peaks (441) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 441 pairs to build model! INFO @ Fri, 10 Dec 2021 13:26:42: start model_add_line... INFO @ Fri, 10 Dec 2021 13:26:42: start X-correlation... INFO @ Fri, 10 Dec 2021 13:26:42: end of X-cor INFO @ Fri, 10 Dec 2021 13:26:42: #2 finished! INFO @ Fri, 10 Dec 2021 13:26:42: #2 predicted fragment length is 148 bps INFO @ Fri, 10 Dec 2021 13:26:42: #2 alternative fragment length(s) may be 148 bps INFO @ Fri, 10 Dec 2021 13:26:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.20_model.r WARNING @ Fri, 10 Dec 2021 13:26:42: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 13:26:42: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Fri, 10 Dec 2021 13:26:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 13:26:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:26:42: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:27:00: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:27:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:27:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:27:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6407575/SRX6407575.20_summits.bed INFO @ Fri, 10 Dec 2021 13:27:09: Done! pass1 - making usageList (93 chroms): 0 millis pass2 - checking and writing primary data (169 records, 4 fields): 4 millis CompletedMACS2peakCalling