Job ID = 16439499 SRX = SRX13227888 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: 00:12:59 34081160 reads; of these: 34081160 (100.00%) were unpaired; of these: 986270 (2.89%) aligned 0 times 23847471 (69.97%) aligned exactly 1 time 9247419 (27.13%) aligned >1 times 97.11% overall alignment rate Time searching: 00:12:59 Overall time: 00:12:59 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 16 files... [bam_rmdupse_core] 5405090 / 33094890 = 0.1633 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 15:44:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.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 15:44:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:44:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:44:42: 1000000 INFO @ Tue, 02 Aug 2022 15:44:48: 2000000 INFO @ Tue, 02 Aug 2022 15:44:55: 3000000 INFO @ Tue, 02 Aug 2022 15:45:01: 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 15:45:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.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 15:45:05: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:45:05: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:45:07: 5000000 INFO @ Tue, 02 Aug 2022 15:45:12: 1000000 INFO @ Tue, 02 Aug 2022 15:45:14: 6000000 INFO @ Tue, 02 Aug 2022 15:45:18: 2000000 INFO @ Tue, 02 Aug 2022 15:45:20: 7000000 INFO @ Tue, 02 Aug 2022 15:45:25: 3000000 INFO @ Tue, 02 Aug 2022 15:45:27: 8000000 INFO @ Tue, 02 Aug 2022 15:45:32: 4000000 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 15:45:34: 9000000 INFO @ Tue, 02 Aug 2022 15:45:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.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 15:45:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:45:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:45:38: 5000000 INFO @ Tue, 02 Aug 2022 15:45:41: 10000000 INFO @ Tue, 02 Aug 2022 15:45:42: 1000000 INFO @ Tue, 02 Aug 2022 15:45:45: 6000000 INFO @ Tue, 02 Aug 2022 15:45:47: 11000000 INFO @ Tue, 02 Aug 2022 15:45:49: 2000000 INFO @ Tue, 02 Aug 2022 15:45:52: 7000000 INFO @ Tue, 02 Aug 2022 15:45:54: 12000000 INFO @ Tue, 02 Aug 2022 15:45:56: 3000000 INFO @ Tue, 02 Aug 2022 15:45:59: 8000000 INFO @ Tue, 02 Aug 2022 15:46:00: 13000000 INFO @ Tue, 02 Aug 2022 15:46:03: 4000000 INFO @ Tue, 02 Aug 2022 15:46:05: 9000000 INFO @ Tue, 02 Aug 2022 15:46:07: 14000000 INFO @ Tue, 02 Aug 2022 15:46:09: 5000000 INFO @ Tue, 02 Aug 2022 15:46:12: 10000000 INFO @ Tue, 02 Aug 2022 15:46:14: 15000000 INFO @ Tue, 02 Aug 2022 15:46:16: 6000000 INFO @ Tue, 02 Aug 2022 15:46:19: 11000000 INFO @ Tue, 02 Aug 2022 15:46:21: 16000000 INFO @ Tue, 02 Aug 2022 15:46:23: 7000000 INFO @ Tue, 02 Aug 2022 15:46:26: 12000000 INFO @ Tue, 02 Aug 2022 15:46:28: 17000000 INFO @ Tue, 02 Aug 2022 15:46:30: 8000000 INFO @ Tue, 02 Aug 2022 15:46:32: 13000000 INFO @ Tue, 02 Aug 2022 15:46:34: 18000000 INFO @ Tue, 02 Aug 2022 15:46:36: 9000000 INFO @ Tue, 02 Aug 2022 15:46:39: 14000000 INFO @ Tue, 02 Aug 2022 15:46:41: 19000000 INFO @ Tue, 02 Aug 2022 15:46:43: 10000000 INFO @ Tue, 02 Aug 2022 15:46:46: 15000000 INFO @ Tue, 02 Aug 2022 15:46:48: 20000000 INFO @ Tue, 02 Aug 2022 15:46:50: 11000000 INFO @ Tue, 02 Aug 2022 15:46:53: 16000000 INFO @ Tue, 02 Aug 2022 15:46:55: 21000000 INFO @ Tue, 02 Aug 2022 15:46:56: 12000000 INFO @ Tue, 02 Aug 2022 15:47:00: 17000000 INFO @ Tue, 02 Aug 2022 15:47:01: 22000000 INFO @ Tue, 02 Aug 2022 15:47:03: 13000000 INFO @ Tue, 02 Aug 2022 15:47:07: 18000000 INFO @ Tue, 02 Aug 2022 15:47:08: 23000000 INFO @ Tue, 02 Aug 2022 15:47:10: 14000000 INFO @ Tue, 02 Aug 2022 15:47:13: 19000000 INFO @ Tue, 02 Aug 2022 15:47:15: 24000000 INFO @ Tue, 02 Aug 2022 15:47:17: 15000000 INFO @ Tue, 02 Aug 2022 15:47:20: 20000000 INFO @ Tue, 02 Aug 2022 15:47:22: 25000000 INFO @ Tue, 02 Aug 2022 15:47:24: 16000000 INFO @ Tue, 02 Aug 2022 15:47:27: 21000000 INFO @ Tue, 02 Aug 2022 15:47:28: 26000000 INFO @ Tue, 02 Aug 2022 15:47:31: 17000000 INFO @ Tue, 02 Aug 2022 15:47:34: 22000000 INFO @ Tue, 02 Aug 2022 15:47:35: 27000000 INFO @ Tue, 02 Aug 2022 15:47:37: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:47:40: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:47:40: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:47:40: #1 total tags in treatment: 27689800 INFO @ Tue, 02 Aug 2022 15:47:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:47:40: #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 15:47:40: #1 tags after filtering in treatment: 27689800 INFO @ Tue, 02 Aug 2022 15:47:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:47:40: #1 finished! INFO @ Tue, 02 Aug 2022 15:47:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:47:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:47:41: 23000000 INFO @ Tue, 02 Aug 2022 15:47:42: #2 number of paired peaks: 311 WARNING @ Tue, 02 Aug 2022 15:47:42: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Tue, 02 Aug 2022 15:47:42: start model_add_line... INFO @ Tue, 02 Aug 2022 15:47:42: start X-correlation... INFO @ Tue, 02 Aug 2022 15:47:42: end of X-cor INFO @ Tue, 02 Aug 2022 15:47:42: #2 finished! INFO @ Tue, 02 Aug 2022 15:47:42: #2 predicted fragment length is 3 bps INFO @ Tue, 02 Aug 2022 15:47:42: #2 alternative fragment length(s) may be 3,25 bps INFO @ Tue, 02 Aug 2022 15:47:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.05_model.r WARNING @ Tue, 02 Aug 2022 15:47:42: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:47:42: #2 You may need to consider one of the other alternative d(s): 3,25 WARNING @ Tue, 02 Aug 2022 15:47:42: #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 15:47:42: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:47:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:47:44: 19000000 INFO @ Tue, 02 Aug 2022 15:47:47: 24000000 INFO @ Tue, 02 Aug 2022 15:47:51: 20000000 INFO @ Tue, 02 Aug 2022 15:47:55: 25000000 INFO @ Tue, 02 Aug 2022 15:47:58: 21000000 INFO @ Tue, 02 Aug 2022 15:48:03: 26000000 INFO @ Tue, 02 Aug 2022 15:48:05: 22000000 INFO @ Tue, 02 Aug 2022 15:48:10: 27000000 INFO @ Tue, 02 Aug 2022 15:48:12: 23000000 INFO @ Tue, 02 Aug 2022 15:48:15: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:48:15: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:48:15: #1 total tags in treatment: 27689800 INFO @ Tue, 02 Aug 2022 15:48:15: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:48:15: #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 15:48:16: #1 tags after filtering in treatment: 27689800 INFO @ Tue, 02 Aug 2022 15:48:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:48:16: #1 finished! INFO @ Tue, 02 Aug 2022 15:48:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:48:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:48:18: #2 number of paired peaks: 311 WARNING @ Tue, 02 Aug 2022 15:48:18: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Tue, 02 Aug 2022 15:48:18: start model_add_line... INFO @ Tue, 02 Aug 2022 15:48:18: start X-correlation... INFO @ Tue, 02 Aug 2022 15:48:18: end of X-cor INFO @ Tue, 02 Aug 2022 15:48:18: #2 finished! INFO @ Tue, 02 Aug 2022 15:48:18: #2 predicted fragment length is 3 bps INFO @ Tue, 02 Aug 2022 15:48:18: #2 alternative fragment length(s) may be 3,25 bps INFO @ Tue, 02 Aug 2022 15:48:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.10_model.r WARNING @ Tue, 02 Aug 2022 15:48:18: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:48:18: #2 You may need to consider one of the other alternative d(s): 3,25 WARNING @ Tue, 02 Aug 2022 15:48:18: #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 15:48:18: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:48:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:48:20: 24000000 INFO @ Tue, 02 Aug 2022 15:48:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:48:26: 25000000 INFO @ Tue, 02 Aug 2022 15:48:32: 26000000 INFO @ Tue, 02 Aug 2022 15:48:38: 27000000 INFO @ Tue, 02 Aug 2022 15:48:42: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:48:42: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:48:42: #1 total tags in treatment: 27689800 INFO @ Tue, 02 Aug 2022 15:48:42: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:48:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:48:43: #1 tags after filtering in treatment: 27689800 INFO @ Tue, 02 Aug 2022 15:48:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:48:43: #1 finished! INFO @ Tue, 02 Aug 2022 15:48:43: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:48:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:48:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:48:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:48:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.05_summits.bed INFO @ Tue, 02 Aug 2022 15:48:45: Done! INFO @ Tue, 02 Aug 2022 15:48:45: #2 number of paired peaks: 311 WARNING @ Tue, 02 Aug 2022 15:48:45: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Tue, 02 Aug 2022 15:48:45: start model_add_line... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:48:45: start X-correlation... INFO @ Tue, 02 Aug 2022 15:48:45: end of X-cor INFO @ Tue, 02 Aug 2022 15:48:45: #2 finished! INFO @ Tue, 02 Aug 2022 15:48:45: #2 predicted fragment length is 3 bps INFO @ Tue, 02 Aug 2022 15:48:45: #2 alternative fragment length(s) may be 3,25 bps INFO @ Tue, 02 Aug 2022 15:48:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.20_model.r WARNING @ Tue, 02 Aug 2022 15:48:45: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:48:45: #2 You may need to consider one of the other alternative d(s): 3,25 WARNING @ Tue, 02 Aug 2022 15:48:45: #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 15:48:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:48:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:49:01: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:49:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:49:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:49:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.10_summits.bed INFO @ Tue, 02 Aug 2022 15:49:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:49:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:49:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:49:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:49:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX13227888/SRX13227888.20_summits.bed INFO @ Tue, 02 Aug 2022 15:49:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling