Job ID = 6529248 SRX = SRX110793 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: 00:06:59 23332337 reads; of these: 23332337 (100.00%) were unpaired; of these: 666565 (2.86%) aligned 0 times 12199527 (52.29%) aligned exactly 1 time 10466245 (44.86%) aligned >1 times 97.14% overall alignment rate Time searching: 00:06:59 Overall time: 00:06:59 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2395963 / 22665772 = 0.1057 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, 30 Jun 2020 02:03:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.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, 30 Jun 2020 02:03:22: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:03:22: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:03:27: 1000000 INFO @ Tue, 30 Jun 2020 02:03:32: 2000000 INFO @ Tue, 30 Jun 2020 02:03:36: 3000000 INFO @ Tue, 30 Jun 2020 02:03:41: 4000000 INFO @ Tue, 30 Jun 2020 02:03:46: 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, 30 Jun 2020 02:03:50: 6000000 INFO @ Tue, 30 Jun 2020 02:03:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.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, 30 Jun 2020 02:03:52: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:03:52: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:03:55: 7000000 INFO @ Tue, 30 Jun 2020 02:03:57: 1000000 INFO @ Tue, 30 Jun 2020 02:04:00: 8000000 INFO @ Tue, 30 Jun 2020 02:04:02: 2000000 INFO @ Tue, 30 Jun 2020 02:04:05: 9000000 INFO @ Tue, 30 Jun 2020 02:04:07: 3000000 INFO @ Tue, 30 Jun 2020 02:04:10: 10000000 INFO @ Tue, 30 Jun 2020 02:04:12: 4000000 INFO @ Tue, 30 Jun 2020 02:04:15: 11000000 INFO @ Tue, 30 Jun 2020 02:04:17: 5000000 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, 30 Jun 2020 02:04:20: 12000000 INFO @ Tue, 30 Jun 2020 02:04:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.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, 30 Jun 2020 02:04:22: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:04:22: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:04:22: 6000000 INFO @ Tue, 30 Jun 2020 02:04:25: 13000000 INFO @ Tue, 30 Jun 2020 02:04:28: 1000000 INFO @ Tue, 30 Jun 2020 02:04:28: 7000000 INFO @ Tue, 30 Jun 2020 02:04:31: 14000000 INFO @ Tue, 30 Jun 2020 02:04:34: 8000000 INFO @ Tue, 30 Jun 2020 02:04:34: 2000000 INFO @ Tue, 30 Jun 2020 02:04:37: 15000000 INFO @ Tue, 30 Jun 2020 02:04:39: 9000000 INFO @ Tue, 30 Jun 2020 02:04:39: 3000000 INFO @ Tue, 30 Jun 2020 02:04:42: 16000000 INFO @ Tue, 30 Jun 2020 02:04:45: 10000000 INFO @ Tue, 30 Jun 2020 02:04:45: 4000000 INFO @ Tue, 30 Jun 2020 02:04:49: 17000000 INFO @ Tue, 30 Jun 2020 02:04:51: 11000000 INFO @ Tue, 30 Jun 2020 02:04:51: 5000000 INFO @ Tue, 30 Jun 2020 02:04:54: 18000000 INFO @ Tue, 30 Jun 2020 02:04:56: 12000000 INFO @ Tue, 30 Jun 2020 02:04:57: 6000000 INFO @ Tue, 30 Jun 2020 02:05:00: 19000000 INFO @ Tue, 30 Jun 2020 02:05:02: 13000000 INFO @ Tue, 30 Jun 2020 02:05:03: 7000000 INFO @ Tue, 30 Jun 2020 02:05:06: 20000000 INFO @ Tue, 30 Jun 2020 02:05:08: #1 tag size is determined as 18 bps INFO @ Tue, 30 Jun 2020 02:05:08: #1 tag size = 18 INFO @ Tue, 30 Jun 2020 02:05:08: #1 total tags in treatment: 20269809 INFO @ Tue, 30 Jun 2020 02:05:08: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:05:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:05:08: 14000000 INFO @ Tue, 30 Jun 2020 02:05:09: 8000000 INFO @ Tue, 30 Jun 2020 02:05:09: #1 tags after filtering in treatment: 20269809 INFO @ Tue, 30 Jun 2020 02:05:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:05:09: #1 finished! INFO @ Tue, 30 Jun 2020 02:05:09: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:05:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:05:10: #2 number of paired peaks: 168 WARNING @ Tue, 30 Jun 2020 02:05:10: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Tue, 30 Jun 2020 02:05:10: start model_add_line... INFO @ Tue, 30 Jun 2020 02:05:10: start X-correlation... INFO @ Tue, 30 Jun 2020 02:05:10: end of X-cor INFO @ Tue, 30 Jun 2020 02:05:10: #2 finished! INFO @ Tue, 30 Jun 2020 02:05:10: #2 predicted fragment length is 31 bps INFO @ Tue, 30 Jun 2020 02:05:10: #2 alternative fragment length(s) may be 4,31 bps INFO @ Tue, 30 Jun 2020 02:05:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.05_model.r WARNING @ Tue, 30 Jun 2020 02:05:10: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:05:10: #2 You may need to consider one of the other alternative d(s): 4,31 WARNING @ Tue, 30 Jun 2020 02:05:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:05:10: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:05:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:05:14: 15000000 INFO @ Tue, 30 Jun 2020 02:05:15: 9000000 INFO @ Tue, 30 Jun 2020 02:05:20: 16000000 INFO @ Tue, 30 Jun 2020 02:05:21: 10000000 INFO @ Tue, 30 Jun 2020 02:05:26: 11000000 INFO @ Tue, 30 Jun 2020 02:05:27: 17000000 INFO @ Tue, 30 Jun 2020 02:05:33: 12000000 INFO @ Tue, 30 Jun 2020 02:05:33: 18000000 INFO @ Tue, 30 Jun 2020 02:05:39: 13000000 INFO @ Tue, 30 Jun 2020 02:05:39: 19000000 INFO @ Tue, 30 Jun 2020 02:05:45: 14000000 INFO @ Tue, 30 Jun 2020 02:05:45: 20000000 INFO @ Tue, 30 Jun 2020 02:05:46: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:05:47: #1 tag size is determined as 18 bps INFO @ Tue, 30 Jun 2020 02:05:47: #1 tag size = 18 INFO @ Tue, 30 Jun 2020 02:05:47: #1 total tags in treatment: 20269809 INFO @ Tue, 30 Jun 2020 02:05:47: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:05:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:05:48: #1 tags after filtering in treatment: 20269809 INFO @ Tue, 30 Jun 2020 02:05:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:05:48: #1 finished! INFO @ Tue, 30 Jun 2020 02:05:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:05:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:05:49: #2 number of paired peaks: 168 WARNING @ Tue, 30 Jun 2020 02:05:49: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Tue, 30 Jun 2020 02:05:49: start model_add_line... INFO @ Tue, 30 Jun 2020 02:05:50: start X-correlation... INFO @ Tue, 30 Jun 2020 02:05:50: end of X-cor INFO @ Tue, 30 Jun 2020 02:05:50: #2 finished! INFO @ Tue, 30 Jun 2020 02:05:50: #2 predicted fragment length is 31 bps INFO @ Tue, 30 Jun 2020 02:05:50: #2 alternative fragment length(s) may be 4,31 bps INFO @ Tue, 30 Jun 2020 02:05:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.10_model.r WARNING @ Tue, 30 Jun 2020 02:05:50: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:05:50: #2 You may need to consider one of the other alternative d(s): 4,31 WARNING @ Tue, 30 Jun 2020 02:05:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:05:50: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:05:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:05:52: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:05:58: 16000000 INFO @ Tue, 30 Jun 2020 02:06:06: 17000000 INFO @ Tue, 30 Jun 2020 02:06:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:06:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:06:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.05_summits.bed INFO @ Tue, 30 Jun 2020 02:06:06: Done! pass1 - making usageList (385 chroms): 3 millis pass2 - checking and writing primary data (2546 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:06:13: 18000000 INFO @ Tue, 30 Jun 2020 02:06:19: 19000000 INFO @ Tue, 30 Jun 2020 02:06:25: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:06:26: 20000000 INFO @ Tue, 30 Jun 2020 02:06:28: #1 tag size is determined as 18 bps INFO @ Tue, 30 Jun 2020 02:06:28: #1 tag size = 18 INFO @ Tue, 30 Jun 2020 02:06:28: #1 total tags in treatment: 20269809 INFO @ Tue, 30 Jun 2020 02:06:28: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:06:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:06:29: #1 tags after filtering in treatment: 20269809 INFO @ Tue, 30 Jun 2020 02:06:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:06:29: #1 finished! INFO @ Tue, 30 Jun 2020 02:06:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:06:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:06:31: #2 number of paired peaks: 168 WARNING @ Tue, 30 Jun 2020 02:06:31: Fewer paired peaks (168) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 168 pairs to build model! INFO @ Tue, 30 Jun 2020 02:06:31: start model_add_line... INFO @ Tue, 30 Jun 2020 02:06:31: start X-correlation... INFO @ Tue, 30 Jun 2020 02:06:31: end of X-cor INFO @ Tue, 30 Jun 2020 02:06:31: #2 finished! INFO @ Tue, 30 Jun 2020 02:06:31: #2 predicted fragment length is 31 bps INFO @ Tue, 30 Jun 2020 02:06:31: #2 alternative fragment length(s) may be 4,31 bps INFO @ Tue, 30 Jun 2020 02:06:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.20_model.r WARNING @ Tue, 30 Jun 2020 02:06:31: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:06:31: #2 You may need to consider one of the other alternative d(s): 4,31 WARNING @ Tue, 30 Jun 2020 02:06:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:06:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:06:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:06:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:06:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:06:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.10_summits.bed INFO @ Tue, 30 Jun 2020 02:06:45: Done! pass1 - making usageList (123 chroms): 1 millis pass2 - checking and writing primary data (442 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:07:06: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:07:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:07:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:07:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110793/SRX110793.20_summits.bed INFO @ Tue, 30 Jun 2020 02:07:26: Done! pass1 - making usageList (75 chroms): 1 millis pass2 - checking and writing primary data (152 records, 4 fields): 5 millis CompletedMACS2peakCalling