Job ID = 14167390 SRX = SRX8574262 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: 00:09:37 39426069 reads; of these: 39426069 (100.00%) were unpaired; of these: 3723011 (9.44%) aligned 0 times 27089600 (68.71%) aligned exactly 1 time 8613458 (21.85%) aligned >1 times 90.56% overall alignment rate Time searching: 00:09:37 Overall time: 00:09:37 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] 14268041 / 35703058 = 0.3996 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 12:22:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.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 12:22:52: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:22:52: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:22:58: 1000000 INFO @ Fri, 10 Dec 2021 12:23:04: 2000000 INFO @ Fri, 10 Dec 2021 12:23:09: 3000000 INFO @ Fri, 10 Dec 2021 12:23:16: 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 12:23:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.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 12:23:20: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:23:20: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:23:23: 5000000 INFO @ Fri, 10 Dec 2021 12:23:26: 1000000 INFO @ Fri, 10 Dec 2021 12:23:29: 6000000 INFO @ Fri, 10 Dec 2021 12:23:33: 2000000 INFO @ Fri, 10 Dec 2021 12:23:37: 7000000 INFO @ Fri, 10 Dec 2021 12:23:40: 3000000 INFO @ Fri, 10 Dec 2021 12:23:43: 8000000 INFO @ Fri, 10 Dec 2021 12:23:47: 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 12:23:50: 9000000 INFO @ Fri, 10 Dec 2021 12:23:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.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 12:23:51: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:23:51: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:23:55: 5000000 INFO @ Fri, 10 Dec 2021 12:23:57: 10000000 INFO @ Fri, 10 Dec 2021 12:23:58: 1000000 INFO @ Fri, 10 Dec 2021 12:24:04: 11000000 INFO @ Fri, 10 Dec 2021 12:24:04: 6000000 INFO @ Fri, 10 Dec 2021 12:24:06: 2000000 INFO @ Fri, 10 Dec 2021 12:24:10: 12000000 INFO @ Fri, 10 Dec 2021 12:24:11: 7000000 INFO @ Fri, 10 Dec 2021 12:24:13: 3000000 INFO @ Fri, 10 Dec 2021 12:24:16: 13000000 INFO @ Fri, 10 Dec 2021 12:24:19: 8000000 INFO @ Fri, 10 Dec 2021 12:24:19: 4000000 INFO @ Fri, 10 Dec 2021 12:24:23: 14000000 INFO @ Fri, 10 Dec 2021 12:24:24: 5000000 INFO @ Fri, 10 Dec 2021 12:24:26: 9000000 INFO @ Fri, 10 Dec 2021 12:24:30: 15000000 INFO @ Fri, 10 Dec 2021 12:24:31: 6000000 INFO @ Fri, 10 Dec 2021 12:24:33: 10000000 INFO @ Fri, 10 Dec 2021 12:24:37: 7000000 INFO @ Fri, 10 Dec 2021 12:24:38: 16000000 INFO @ Fri, 10 Dec 2021 12:24:41: 11000000 INFO @ Fri, 10 Dec 2021 12:24:45: 8000000 INFO @ Fri, 10 Dec 2021 12:24:46: 17000000 INFO @ Fri, 10 Dec 2021 12:24:48: 12000000 INFO @ Fri, 10 Dec 2021 12:24:53: 18000000 INFO @ Fri, 10 Dec 2021 12:24:54: 9000000 INFO @ Fri, 10 Dec 2021 12:24:56: 13000000 INFO @ Fri, 10 Dec 2021 12:24:59: 19000000 INFO @ Fri, 10 Dec 2021 12:25:00: 10000000 INFO @ Fri, 10 Dec 2021 12:25:04: 14000000 INFO @ Fri, 10 Dec 2021 12:25:06: 20000000 INFO @ Fri, 10 Dec 2021 12:25:08: 11000000 INFO @ Fri, 10 Dec 2021 12:25:12: 21000000 INFO @ Fri, 10 Dec 2021 12:25:13: 15000000 INFO @ Fri, 10 Dec 2021 12:25:15: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:25:15: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:25:15: #1 total tags in treatment: 21435017 INFO @ Fri, 10 Dec 2021 12:25:15: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:25:15: #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 12:25:16: 12000000 INFO @ Fri, 10 Dec 2021 12:25:16: #1 tags after filtering in treatment: 21435017 INFO @ Fri, 10 Dec 2021 12:25:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:25:16: #1 finished! INFO @ Fri, 10 Dec 2021 12:25:16: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:25:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:25:18: #2 number of paired peaks: 497 WARNING @ Fri, 10 Dec 2021 12:25:18: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Fri, 10 Dec 2021 12:25:18: start model_add_line... INFO @ Fri, 10 Dec 2021 12:25:18: start X-correlation... INFO @ Fri, 10 Dec 2021 12:25:18: end of X-cor INFO @ Fri, 10 Dec 2021 12:25:18: #2 finished! INFO @ Fri, 10 Dec 2021 12:25:18: #2 predicted fragment length is 2 bps INFO @ Fri, 10 Dec 2021 12:25:18: #2 alternative fragment length(s) may be 2,19 bps INFO @ Fri, 10 Dec 2021 12:25:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.05_model.r WARNING @ Fri, 10 Dec 2021 12:25:18: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:25:18: #2 You may need to consider one of the other alternative d(s): 2,19 WARNING @ Fri, 10 Dec 2021 12:25:18: #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 12:25:18: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:25:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:25:21: 16000000 INFO @ Fri, 10 Dec 2021 12:25:23: 13000000 INFO @ Fri, 10 Dec 2021 12:25:30: 17000000 INFO @ Fri, 10 Dec 2021 12:25:31: 14000000 INFO @ Fri, 10 Dec 2021 12:25:37: 15000000 INFO @ Fri, 10 Dec 2021 12:25:40: 18000000 INFO @ Fri, 10 Dec 2021 12:25:45: 16000000 INFO @ Fri, 10 Dec 2021 12:25:48: 19000000 INFO @ Fri, 10 Dec 2021 12:25:53: 17000000 INFO @ Fri, 10 Dec 2021 12:25:55: 20000000 INFO @ Fri, 10 Dec 2021 12:26:01: 18000000 INFO @ Fri, 10 Dec 2021 12:26:02: 21000000 INFO @ Fri, 10 Dec 2021 12:26:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:26:06: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:26:06: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:26:06: #1 total tags in treatment: 21435017 INFO @ Fri, 10 Dec 2021 12:26:06: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:26:06: #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 12:26:06: #1 tags after filtering in treatment: 21435017 INFO @ Fri, 10 Dec 2021 12:26:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:26:06: #1 finished! INFO @ Fri, 10 Dec 2021 12:26:06: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:26:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:26:07: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:26:08: #2 number of paired peaks: 497 WARNING @ Fri, 10 Dec 2021 12:26:08: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Fri, 10 Dec 2021 12:26:08: start model_add_line... INFO @ Fri, 10 Dec 2021 12:26:08: start X-correlation... INFO @ Fri, 10 Dec 2021 12:26:08: end of X-cor INFO @ Fri, 10 Dec 2021 12:26:08: #2 finished! INFO @ Fri, 10 Dec 2021 12:26:08: #2 predicted fragment length is 2 bps INFO @ Fri, 10 Dec 2021 12:26:08: #2 alternative fragment length(s) may be 2,19 bps INFO @ Fri, 10 Dec 2021 12:26:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.10_model.r WARNING @ Fri, 10 Dec 2021 12:26:08: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:26:08: #2 You may need to consider one of the other alternative d(s): 2,19 WARNING @ Fri, 10 Dec 2021 12:26:08: #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 12:26:08: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:26:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:26:14: 20000000 INFO @ Fri, 10 Dec 2021 12:26:21: 21000000 INFO @ Fri, 10 Dec 2021 12:26:24: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:26:24: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:26:24: #1 total tags in treatment: 21435017 INFO @ Fri, 10 Dec 2021 12:26:24: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:26:24: #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 12:26:25: #1 tags after filtering in treatment: 21435017 INFO @ Fri, 10 Dec 2021 12:26:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:26:25: #1 finished! INFO @ Fri, 10 Dec 2021 12:26:25: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:26:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:26:27: #2 number of paired peaks: 497 WARNING @ Fri, 10 Dec 2021 12:26:27: Fewer paired peaks (497) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 497 pairs to build model! INFO @ Fri, 10 Dec 2021 12:26:27: start model_add_line... INFO @ Fri, 10 Dec 2021 12:26:27: start X-correlation... INFO @ Fri, 10 Dec 2021 12:26:27: end of X-cor INFO @ Fri, 10 Dec 2021 12:26:27: #2 finished! INFO @ Fri, 10 Dec 2021 12:26:27: #2 predicted fragment length is 2 bps INFO @ Fri, 10 Dec 2021 12:26:27: #2 alternative fragment length(s) may be 2,19 bps INFO @ Fri, 10 Dec 2021 12:26:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.20_model.r WARNING @ Fri, 10 Dec 2021 12:26:27: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:26:27: #2 You may need to consider one of the other alternative d(s): 2,19 WARNING @ Fri, 10 Dec 2021 12:26:27: #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 12:26:27: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:26:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:26:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:26:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:26:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.05_summits.bed INFO @ Fri, 10 Dec 2021 12:26:29: Done! pass1 - making usageList (0 chroms): 45 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:26:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:27:13: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:27:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:27:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:27:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.10_summits.bed INFO @ Fri, 10 Dec 2021 12:27:14: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:27:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:27:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:27:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8574262/SRX8574262.20_summits.bed INFO @ Fri, 10 Dec 2021 12:27:37: Done! pass1 - making usageList (0 chroms): 42 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling