Job ID = 6529593 SRX = SRX331402 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: 00:04:38 18463214 reads; of these: 18463214 (100.00%) were unpaired; of these: 1328543 (7.20%) aligned 0 times 13473508 (72.97%) aligned exactly 1 time 3661163 (19.83%) aligned >1 times 92.80% overall alignment rate Time searching: 00:04:38 Overall time: 00:04:38 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] 1541920 / 17134671 = 0.0900 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 02:31:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.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 02:31:08: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:31:08: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:31:14: 1000000 INFO @ Tue, 30 Jun 2020 02:31:20: 2000000 INFO @ Tue, 30 Jun 2020 02:31:25: 3000000 INFO @ Tue, 30 Jun 2020 02:31:31: 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 @ Tue, 30 Jun 2020 02:31:37: 5000000 INFO @ Tue, 30 Jun 2020 02:31:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.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 02:31:38: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:31:38: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:31:44: 6000000 INFO @ Tue, 30 Jun 2020 02:31:46: 1000000 INFO @ Tue, 30 Jun 2020 02:31:51: 7000000 INFO @ Tue, 30 Jun 2020 02:31:54: 2000000 INFO @ Tue, 30 Jun 2020 02:31:58: 8000000 INFO @ Tue, 30 Jun 2020 02:32:02: 3000000 INFO @ Tue, 30 Jun 2020 02:32:05: 9000000 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 02:32:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.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 02:32:08: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:32:08: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:32:11: 4000000 INFO @ Tue, 30 Jun 2020 02:32:13: 10000000 INFO @ Tue, 30 Jun 2020 02:32:17: 1000000 INFO @ Tue, 30 Jun 2020 02:32:19: 5000000 INFO @ Tue, 30 Jun 2020 02:32:20: 11000000 INFO @ Tue, 30 Jun 2020 02:32:25: 2000000 INFO @ Tue, 30 Jun 2020 02:32:27: 6000000 INFO @ Tue, 30 Jun 2020 02:32:28: 12000000 INFO @ Tue, 30 Jun 2020 02:32:34: 3000000 INFO @ Tue, 30 Jun 2020 02:32:36: 7000000 INFO @ Tue, 30 Jun 2020 02:32:36: 13000000 INFO @ Tue, 30 Jun 2020 02:32:43: 4000000 INFO @ Tue, 30 Jun 2020 02:32:44: 14000000 INFO @ Tue, 30 Jun 2020 02:32:44: 8000000 INFO @ Tue, 30 Jun 2020 02:32:51: 15000000 INFO @ Tue, 30 Jun 2020 02:32:51: 5000000 INFO @ Tue, 30 Jun 2020 02:32:53: 9000000 INFO @ Tue, 30 Jun 2020 02:32:56: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:32:56: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:32:56: #1 total tags in treatment: 15592751 INFO @ Tue, 30 Jun 2020 02:32:56: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:32:56: #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 02:32:57: #1 tags after filtering in treatment: 15592750 INFO @ Tue, 30 Jun 2020 02:32:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:32:57: #1 finished! INFO @ Tue, 30 Jun 2020 02:32:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:32:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:32:58: #2 number of paired peaks: 220 WARNING @ Tue, 30 Jun 2020 02:32:58: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Tue, 30 Jun 2020 02:32:58: start model_add_line... INFO @ Tue, 30 Jun 2020 02:32:58: start X-correlation... INFO @ Tue, 30 Jun 2020 02:32:58: end of X-cor INFO @ Tue, 30 Jun 2020 02:32:58: #2 finished! INFO @ Tue, 30 Jun 2020 02:32:58: #2 predicted fragment length is 43 bps INFO @ Tue, 30 Jun 2020 02:32:58: #2 alternative fragment length(s) may be 3,43,554 bps INFO @ Tue, 30 Jun 2020 02:32:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.05_model.r WARNING @ Tue, 30 Jun 2020 02:32:58: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:32:58: #2 You may need to consider one of the other alternative d(s): 3,43,554 WARNING @ Tue, 30 Jun 2020 02:32:58: #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 02:32:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:32:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:33:00: 6000000 INFO @ Tue, 30 Jun 2020 02:33:01: 10000000 INFO @ Tue, 30 Jun 2020 02:33:09: 7000000 INFO @ Tue, 30 Jun 2020 02:33:10: 11000000 INFO @ Tue, 30 Jun 2020 02:33:17: 8000000 INFO @ Tue, 30 Jun 2020 02:33:18: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:33:26: 9000000 INFO @ Tue, 30 Jun 2020 02:33:27: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:33:27: 13000000 INFO @ Tue, 30 Jun 2020 02:33:34: 10000000 INFO @ Tue, 30 Jun 2020 02:33:36: 14000000 INFO @ Tue, 30 Jun 2020 02:33:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:33:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:33:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.05_summits.bed INFO @ Tue, 30 Jun 2020 02:33:41: Done! pass1 - making usageList (505 chroms): 1 millis pass2 - checking and writing primary data (1997 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:33:43: 11000000 INFO @ Tue, 30 Jun 2020 02:33:44: 15000000 INFO @ Tue, 30 Jun 2020 02:33:50: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:33:50: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:33:50: #1 total tags in treatment: 15592751 INFO @ Tue, 30 Jun 2020 02:33:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:33:50: #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 02:33:50: #1 tags after filtering in treatment: 15592750 INFO @ Tue, 30 Jun 2020 02:33:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:33:50: #1 finished! INFO @ Tue, 30 Jun 2020 02:33:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:33:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:33:51: #2 number of paired peaks: 220 WARNING @ Tue, 30 Jun 2020 02:33:51: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Tue, 30 Jun 2020 02:33:51: start model_add_line... INFO @ Tue, 30 Jun 2020 02:33:51: start X-correlation... INFO @ Tue, 30 Jun 2020 02:33:51: end of X-cor INFO @ Tue, 30 Jun 2020 02:33:51: #2 finished! INFO @ Tue, 30 Jun 2020 02:33:51: #2 predicted fragment length is 43 bps INFO @ Tue, 30 Jun 2020 02:33:51: #2 alternative fragment length(s) may be 3,43,554 bps INFO @ Tue, 30 Jun 2020 02:33:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.10_model.r WARNING @ Tue, 30 Jun 2020 02:33:51: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:33:51: #2 You may need to consider one of the other alternative d(s): 3,43,554 WARNING @ Tue, 30 Jun 2020 02:33:51: #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 02:33:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:33:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:33:51: 12000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:34:00: 13000000 INFO @ Tue, 30 Jun 2020 02:34:08: 14000000 INFO @ Tue, 30 Jun 2020 02:34:15: 15000000 INFO @ Tue, 30 Jun 2020 02:34:20: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:34:20: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:34:20: #1 total tags in treatment: 15592751 INFO @ Tue, 30 Jun 2020 02:34:20: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:34:20: #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 02:34:20: #1 tags after filtering in treatment: 15592750 INFO @ Tue, 30 Jun 2020 02:34:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:34:20: #1 finished! INFO @ Tue, 30 Jun 2020 02:34:20: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:34:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:34:21: #2 number of paired peaks: 220 WARNING @ Tue, 30 Jun 2020 02:34:21: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Tue, 30 Jun 2020 02:34:21: start model_add_line... INFO @ Tue, 30 Jun 2020 02:34:22: start X-correlation... INFO @ Tue, 30 Jun 2020 02:34:22: end of X-cor INFO @ Tue, 30 Jun 2020 02:34:22: #2 finished! INFO @ Tue, 30 Jun 2020 02:34:22: #2 predicted fragment length is 43 bps INFO @ Tue, 30 Jun 2020 02:34:22: #2 alternative fragment length(s) may be 3,43,554 bps INFO @ Tue, 30 Jun 2020 02:34:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.20_model.r WARNING @ Tue, 30 Jun 2020 02:34:22: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:34:22: #2 You may need to consider one of the other alternative d(s): 3,43,554 WARNING @ Tue, 30 Jun 2020 02:34:22: #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 02:34:22: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:34:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:34:24: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:34:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:34:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:34:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.10_summits.bed INFO @ Tue, 30 Jun 2020 02:34:40: Done! pass1 - making usageList (366 chroms): 2 millis pass2 - checking and writing primary data (985 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:34:54: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:35:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:35:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:35:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331402/SRX331402.20_summits.bed INFO @ Tue, 30 Jun 2020 02:35:09: Done! pass1 - making usageList (168 chroms): 1 millis pass2 - checking and writing primary data (360 records, 4 fields): 8 millis CompletedMACS2peakCalling