Job ID = 16439492 SRX = SRX13227898 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: 00:14:07 39029700 reads; of these: 39029700 (100.00%) were unpaired; of these: 1185860 (3.04%) aligned 0 times 27344068 (70.06%) aligned exactly 1 time 10499772 (26.90%) aligned >1 times 96.96% overall alignment rate Time searching: 00:14:07 Overall time: 00:14:07 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 16 files... [bam_rmdupse_core] 6598884 / 37843840 = 0.1744 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:44:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.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, 02 Aug 2022 15:44:39: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:44:39: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:44:46: 1000000 INFO @ Tue, 02 Aug 2022 15:44:52: 2000000 INFO @ Tue, 02 Aug 2022 15:44:59: 3000000 INFO @ Tue, 02 Aug 2022 15:45:05: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:45:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.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, 02 Aug 2022 15:45:07: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:45:07: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:45:12: 5000000 INFO @ Tue, 02 Aug 2022 15:45:15: 1000000 INFO @ Tue, 02 Aug 2022 15:45:20: 6000000 INFO @ Tue, 02 Aug 2022 15:45:23: 2000000 INFO @ Tue, 02 Aug 2022 15:45:27: 7000000 INFO @ Tue, 02 Aug 2022 15:45:30: 3000000 INFO @ Tue, 02 Aug 2022 15:45:34: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:45:37: 4000000 INFO @ Tue, 02 Aug 2022 15:45:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.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, 02 Aug 2022 15:45:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:45:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:45:42: 9000000 INFO @ Tue, 02 Aug 2022 15:45:45: 5000000 INFO @ Tue, 02 Aug 2022 15:45:45: 1000000 INFO @ Tue, 02 Aug 2022 15:45:49: 10000000 INFO @ Tue, 02 Aug 2022 15:45:52: 2000000 INFO @ Tue, 02 Aug 2022 15:45:52: 6000000 INFO @ Tue, 02 Aug 2022 15:45:57: 11000000 INFO @ Tue, 02 Aug 2022 15:45:59: 3000000 INFO @ Tue, 02 Aug 2022 15:46:00: 7000000 INFO @ Tue, 02 Aug 2022 15:46:04: 12000000 INFO @ Tue, 02 Aug 2022 15:46:07: 4000000 INFO @ Tue, 02 Aug 2022 15:46:07: 8000000 INFO @ Tue, 02 Aug 2022 15:46:12: 13000000 INFO @ Tue, 02 Aug 2022 15:46:14: 5000000 INFO @ Tue, 02 Aug 2022 15:46:15: 9000000 INFO @ Tue, 02 Aug 2022 15:46:19: 14000000 INFO @ Tue, 02 Aug 2022 15:46:21: 6000000 INFO @ Tue, 02 Aug 2022 15:46:22: 10000000 INFO @ Tue, 02 Aug 2022 15:46:26: 15000000 INFO @ Tue, 02 Aug 2022 15:46:29: 7000000 INFO @ Tue, 02 Aug 2022 15:46:30: 11000000 INFO @ Tue, 02 Aug 2022 15:46:33: 16000000 INFO @ Tue, 02 Aug 2022 15:46:36: 8000000 INFO @ Tue, 02 Aug 2022 15:46:38: 12000000 INFO @ Tue, 02 Aug 2022 15:46:41: 17000000 INFO @ Tue, 02 Aug 2022 15:46:43: 9000000 INFO @ Tue, 02 Aug 2022 15:46:45: 13000000 INFO @ Tue, 02 Aug 2022 15:46:48: 18000000 INFO @ Tue, 02 Aug 2022 15:46:51: 10000000 INFO @ Tue, 02 Aug 2022 15:46:53: 14000000 INFO @ Tue, 02 Aug 2022 15:46:55: 19000000 INFO @ Tue, 02 Aug 2022 15:46:58: 11000000 INFO @ Tue, 02 Aug 2022 15:47:00: 15000000 INFO @ Tue, 02 Aug 2022 15:47:03: 20000000 INFO @ Tue, 02 Aug 2022 15:47:05: 12000000 INFO @ Tue, 02 Aug 2022 15:47:07: 16000000 INFO @ Tue, 02 Aug 2022 15:47:10: 21000000 INFO @ Tue, 02 Aug 2022 15:47:13: 13000000 INFO @ Tue, 02 Aug 2022 15:47:15: 17000000 INFO @ Tue, 02 Aug 2022 15:47:18: 22000000 INFO @ Tue, 02 Aug 2022 15:47:20: 14000000 INFO @ Tue, 02 Aug 2022 15:47:22: 18000000 INFO @ Tue, 02 Aug 2022 15:47:25: 23000000 INFO @ Tue, 02 Aug 2022 15:47:27: 15000000 INFO @ Tue, 02 Aug 2022 15:47:29: 19000000 INFO @ Tue, 02 Aug 2022 15:47:32: 24000000 INFO @ Tue, 02 Aug 2022 15:47:34: 16000000 INFO @ Tue, 02 Aug 2022 15:47:36: 20000000 INFO @ Tue, 02 Aug 2022 15:47:40: 25000000 INFO @ Tue, 02 Aug 2022 15:47:42: 17000000 INFO @ Tue, 02 Aug 2022 15:47:43: 21000000 INFO @ Tue, 02 Aug 2022 15:47:47: 26000000 INFO @ Tue, 02 Aug 2022 15:47:49: 18000000 INFO @ Tue, 02 Aug 2022 15:47:51: 22000000 INFO @ Tue, 02 Aug 2022 15:47:55: 27000000 INFO @ Tue, 02 Aug 2022 15:47:56: 19000000 INFO @ Tue, 02 Aug 2022 15:47:58: 23000000 INFO @ Tue, 02 Aug 2022 15:48:02: 28000000 INFO @ Tue, 02 Aug 2022 15:48:03: 20000000 INFO @ Tue, 02 Aug 2022 15:48:05: 24000000 INFO @ Tue, 02 Aug 2022 15:48:09: 29000000 INFO @ Tue, 02 Aug 2022 15:48:10: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:48:12: 25000000 INFO @ Tue, 02 Aug 2022 15:48:16: 30000000 INFO @ Tue, 02 Aug 2022 15:48:17: 22000000 INFO @ Tue, 02 Aug 2022 15:48:20: 26000000 INFO @ Tue, 02 Aug 2022 15:48:24: 31000000 INFO @ Tue, 02 Aug 2022 15:48:24: 23000000 INFO @ Tue, 02 Aug 2022 15:48:26: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:48:26: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:48:26: #1 total tags in treatment: 31244956 INFO @ Tue, 02 Aug 2022 15:48:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:48:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:48:27: #1 tags after filtering in treatment: 31244956 INFO @ Tue, 02 Aug 2022 15:48:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:48:27: #1 finished! INFO @ Tue, 02 Aug 2022 15:48:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:48:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:48:27: 27000000 INFO @ Tue, 02 Aug 2022 15:48:29: #2 number of paired peaks: 216 WARNING @ Tue, 02 Aug 2022 15:48:29: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Tue, 02 Aug 2022 15:48:29: start model_add_line... INFO @ Tue, 02 Aug 2022 15:48:29: start X-correlation... INFO @ Tue, 02 Aug 2022 15:48:29: end of X-cor INFO @ Tue, 02 Aug 2022 15:48:29: #2 finished! INFO @ Tue, 02 Aug 2022 15:48:29: #2 predicted fragment length is 2 bps INFO @ Tue, 02 Aug 2022 15:48:29: #2 alternative fragment length(s) may be 2,25 bps INFO @ Tue, 02 Aug 2022 15:48:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.05_model.r WARNING @ Tue, 02 Aug 2022 15:48:29: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:48:29: #2 You may need to consider one of the other alternative d(s): 2,25 WARNING @ Tue, 02 Aug 2022 15:48:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:48:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:48:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:48:31: 24000000 INFO @ Tue, 02 Aug 2022 15:48:34: 28000000 INFO @ Tue, 02 Aug 2022 15:48:39: 25000000 INFO @ Tue, 02 Aug 2022 15:48:41: 29000000 INFO @ Tue, 02 Aug 2022 15:48:46: 26000000 INFO @ Tue, 02 Aug 2022 15:48:48: 30000000 INFO @ Tue, 02 Aug 2022 15:48:54: 27000000 INFO @ Tue, 02 Aug 2022 15:48:55: 31000000 INFO @ Tue, 02 Aug 2022 15:48:57: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:48:57: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:48:57: #1 total tags in treatment: 31244956 INFO @ Tue, 02 Aug 2022 15:48:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:48:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:48:58: #1 tags after filtering in treatment: 31244956 INFO @ Tue, 02 Aug 2022 15:48:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:48:58: #1 finished! INFO @ Tue, 02 Aug 2022 15:48:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:48:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:49:00: #2 number of paired peaks: 216 WARNING @ Tue, 02 Aug 2022 15:49:00: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Tue, 02 Aug 2022 15:49:00: start model_add_line... INFO @ Tue, 02 Aug 2022 15:49:01: start X-correlation... INFO @ Tue, 02 Aug 2022 15:49:01: end of X-cor INFO @ Tue, 02 Aug 2022 15:49:01: #2 finished! INFO @ Tue, 02 Aug 2022 15:49:01: #2 predicted fragment length is 2 bps INFO @ Tue, 02 Aug 2022 15:49:01: #2 alternative fragment length(s) may be 2,25 bps INFO @ Tue, 02 Aug 2022 15:49:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.10_model.r WARNING @ Tue, 02 Aug 2022 15:49:01: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:49:01: #2 You may need to consider one of the other alternative d(s): 2,25 WARNING @ Tue, 02 Aug 2022 15:49:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:49:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:49:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:49:01: 28000000 INFO @ Tue, 02 Aug 2022 15:49:08: 29000000 INFO @ Tue, 02 Aug 2022 15:49:15: 30000000 INFO @ Tue, 02 Aug 2022 15:49:20: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:49:21: 31000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:49:23: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:49:23: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:49:23: #1 total tags in treatment: 31244956 INFO @ Tue, 02 Aug 2022 15:49:23: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:49:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:49:24: #1 tags after filtering in treatment: 31244956 INFO @ Tue, 02 Aug 2022 15:49:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:49:24: #1 finished! INFO @ Tue, 02 Aug 2022 15:49:24: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:49:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:49:26: #2 number of paired peaks: 216 WARNING @ Tue, 02 Aug 2022 15:49:26: Fewer paired peaks (216) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 216 pairs to build model! INFO @ Tue, 02 Aug 2022 15:49:26: start model_add_line... INFO @ Tue, 02 Aug 2022 15:49:26: start X-correlation... INFO @ Tue, 02 Aug 2022 15:49:26: end of X-cor INFO @ Tue, 02 Aug 2022 15:49:26: #2 finished! INFO @ Tue, 02 Aug 2022 15:49:26: #2 predicted fragment length is 2 bps INFO @ Tue, 02 Aug 2022 15:49:26: #2 alternative fragment length(s) may be 2,25 bps INFO @ Tue, 02 Aug 2022 15:49:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.20_model.r WARNING @ Tue, 02 Aug 2022 15:49:26: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:49:26: #2 You may need to consider one of the other alternative d(s): 2,25 WARNING @ Tue, 02 Aug 2022 15:49:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:49:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:49:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:49:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:49:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:49:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.05_summits.bed INFO @ Tue, 02 Aug 2022 15:49:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:49:51: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:50:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:50:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:50:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.10_summits.bed INFO @ Tue, 02 Aug 2022 15:50:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:50:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:50:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:50:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:50:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227898/SRX13227898.20_summits.bed INFO @ Tue, 02 Aug 2022 15:50:38: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling