Job ID = 6529355 SRX = SRX201892 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: 00:08:35 32007439 reads; of these: 32007439 (100.00%) were unpaired; of these: 1106173 (3.46%) aligned 0 times 22739669 (71.04%) aligned exactly 1 time 8161597 (25.50%) aligned >1 times 96.54% overall alignment rate Time searching: 00:08:35 Overall time: 00:08:35 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] 6289570 / 30901266 = 0.2035 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 02:09:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.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 02:09:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:09:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:09:30: 1000000 INFO @ Tue, 30 Jun 2020 02:09:37: 2000000 INFO @ Tue, 30 Jun 2020 02:09:44: 3000000 INFO @ Tue, 30 Jun 2020 02:09:51: 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 02:09:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.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 02:09:53: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:09:53: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:09:58: 5000000 INFO @ Tue, 30 Jun 2020 02:10:01: 1000000 INFO @ Tue, 30 Jun 2020 02:10:05: 6000000 INFO @ Tue, 30 Jun 2020 02:10:07: 2000000 INFO @ Tue, 30 Jun 2020 02:10:12: 7000000 INFO @ Tue, 30 Jun 2020 02:10:15: 3000000 INFO @ Tue, 30 Jun 2020 02:10:19: 8000000 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 02:10:22: 4000000 INFO @ Tue, 30 Jun 2020 02:10:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.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 02:10:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:10:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:10:26: 9000000 INFO @ Tue, 30 Jun 2020 02:10:29: 5000000 INFO @ Tue, 30 Jun 2020 02:10:30: 1000000 INFO @ Tue, 30 Jun 2020 02:10:33: 10000000 INFO @ Tue, 30 Jun 2020 02:10:36: 6000000 INFO @ Tue, 30 Jun 2020 02:10:36: 2000000 INFO @ Tue, 30 Jun 2020 02:10:41: 11000000 INFO @ Tue, 30 Jun 2020 02:10:43: 3000000 INFO @ Tue, 30 Jun 2020 02:10:44: 7000000 INFO @ Tue, 30 Jun 2020 02:10:48: 12000000 INFO @ Tue, 30 Jun 2020 02:10:50: 4000000 INFO @ Tue, 30 Jun 2020 02:10:51: 8000000 INFO @ Tue, 30 Jun 2020 02:10:55: 13000000 INFO @ Tue, 30 Jun 2020 02:10:56: 5000000 INFO @ Tue, 30 Jun 2020 02:10:58: 9000000 INFO @ Tue, 30 Jun 2020 02:11:03: 6000000 INFO @ Tue, 30 Jun 2020 02:11:03: 14000000 INFO @ Tue, 30 Jun 2020 02:11:06: 10000000 INFO @ Tue, 30 Jun 2020 02:11:09: 7000000 INFO @ Tue, 30 Jun 2020 02:11:10: 15000000 INFO @ Tue, 30 Jun 2020 02:11:13: 11000000 INFO @ Tue, 30 Jun 2020 02:11:16: 8000000 INFO @ Tue, 30 Jun 2020 02:11:18: 16000000 INFO @ Tue, 30 Jun 2020 02:11:21: 12000000 INFO @ Tue, 30 Jun 2020 02:11:22: 9000000 INFO @ Tue, 30 Jun 2020 02:11:26: 17000000 INFO @ Tue, 30 Jun 2020 02:11:28: 13000000 INFO @ Tue, 30 Jun 2020 02:11:29: 10000000 INFO @ Tue, 30 Jun 2020 02:11:33: 18000000 INFO @ Tue, 30 Jun 2020 02:11:36: 11000000 INFO @ Tue, 30 Jun 2020 02:11:36: 14000000 INFO @ Tue, 30 Jun 2020 02:11:41: 19000000 INFO @ Tue, 30 Jun 2020 02:11:42: 12000000 INFO @ Tue, 30 Jun 2020 02:11:43: 15000000 INFO @ Tue, 30 Jun 2020 02:11:49: 13000000 INFO @ Tue, 30 Jun 2020 02:11:49: 20000000 INFO @ Tue, 30 Jun 2020 02:11:51: 16000000 INFO @ Tue, 30 Jun 2020 02:11:56: 14000000 INFO @ Tue, 30 Jun 2020 02:11:57: 21000000 INFO @ Tue, 30 Jun 2020 02:11:58: 17000000 INFO @ Tue, 30 Jun 2020 02:12:02: 15000000 INFO @ Tue, 30 Jun 2020 02:12:04: 22000000 INFO @ Tue, 30 Jun 2020 02:12:06: 18000000 INFO @ Tue, 30 Jun 2020 02:12:09: 16000000 INFO @ Tue, 30 Jun 2020 02:12:12: 23000000 INFO @ Tue, 30 Jun 2020 02:12:14: 19000000 INFO @ Tue, 30 Jun 2020 02:12:16: 17000000 INFO @ Tue, 30 Jun 2020 02:12:19: 24000000 INFO @ Tue, 30 Jun 2020 02:12:22: 20000000 INFO @ Tue, 30 Jun 2020 02:12:22: 18000000 INFO @ Tue, 30 Jun 2020 02:12:24: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:12:24: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:12:24: #1 total tags in treatment: 24611696 INFO @ Tue, 30 Jun 2020 02:12:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:12:24: #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 02:12:25: #1 tags after filtering in treatment: 24611595 INFO @ Tue, 30 Jun 2020 02:12:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:12:25: #1 finished! INFO @ Tue, 30 Jun 2020 02:12:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:12:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:12:27: #2 number of paired peaks: 723 WARNING @ Tue, 30 Jun 2020 02:12:27: Fewer paired peaks (723) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 723 pairs to build model! INFO @ Tue, 30 Jun 2020 02:12:27: start model_add_line... INFO @ Tue, 30 Jun 2020 02:12:27: start X-correlation... INFO @ Tue, 30 Jun 2020 02:12:27: end of X-cor INFO @ Tue, 30 Jun 2020 02:12:27: #2 finished! INFO @ Tue, 30 Jun 2020 02:12:27: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:12:27: #2 alternative fragment length(s) may be 2,19 bps INFO @ Tue, 30 Jun 2020 02:12:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.05_model.r WARNING @ Tue, 30 Jun 2020 02:12:27: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:12:27: #2 You may need to consider one of the other alternative d(s): 2,19 WARNING @ Tue, 30 Jun 2020 02:12:27: #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 02:12:27: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:12:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:12:29: 21000000 INFO @ Tue, 30 Jun 2020 02:12:29: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:12:36: 22000000 INFO @ Tue, 30 Jun 2020 02:12:36: 20000000 INFO @ Tue, 30 Jun 2020 02:12:42: 23000000 INFO @ Tue, 30 Jun 2020 02:12:43: 21000000 INFO @ Tue, 30 Jun 2020 02:12:49: 24000000 INFO @ Tue, 30 Jun 2020 02:12:50: 22000000 INFO @ Tue, 30 Jun 2020 02:12:54: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:12:54: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:12:54: #1 total tags in treatment: 24611696 INFO @ Tue, 30 Jun 2020 02:12:54: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:12:54: #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 02:12:55: #1 tags after filtering in treatment: 24611595 INFO @ Tue, 30 Jun 2020 02:12:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:12:55: #1 finished! INFO @ Tue, 30 Jun 2020 02:12:55: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:12:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:12:56: 23000000 INFO @ Tue, 30 Jun 2020 02:12:57: #2 number of paired peaks: 723 WARNING @ Tue, 30 Jun 2020 02:12:57: Fewer paired peaks (723) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 723 pairs to build model! INFO @ Tue, 30 Jun 2020 02:12:57: start model_add_line... INFO @ Tue, 30 Jun 2020 02:12:57: start X-correlation... INFO @ Tue, 30 Jun 2020 02:12:57: end of X-cor INFO @ Tue, 30 Jun 2020 02:12:57: #2 finished! INFO @ Tue, 30 Jun 2020 02:12:57: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:12:57: #2 alternative fragment length(s) may be 2,19 bps INFO @ Tue, 30 Jun 2020 02:12:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.10_model.r WARNING @ Tue, 30 Jun 2020 02:12:57: #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, 30 Jun 2020 02:12:57: #2 You may need to consider one of the other alternative d(s): 2,19 WARNING @ Tue, 30 Jun 2020 02:12:57: #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 02:12:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:12:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:13:03: 24000000 INFO @ Tue, 30 Jun 2020 02:13:03: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:13:07: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:13:07: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:13:07: #1 total tags in treatment: 24611696 INFO @ Tue, 30 Jun 2020 02:13:07: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:13:07: #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 02:13:08: #1 tags after filtering in treatment: 24611595 INFO @ Tue, 30 Jun 2020 02:13:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:13:08: #1 finished! INFO @ Tue, 30 Jun 2020 02:13:08: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:13:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:13:10: #2 number of paired peaks: 723 WARNING @ Tue, 30 Jun 2020 02:13:10: Fewer paired peaks (723) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 723 pairs to build model! INFO @ Tue, 30 Jun 2020 02:13:10: start model_add_line... INFO @ Tue, 30 Jun 2020 02:13:10: start X-correlation... INFO @ Tue, 30 Jun 2020 02:13:10: end of X-cor INFO @ Tue, 30 Jun 2020 02:13:10: #2 finished! INFO @ Tue, 30 Jun 2020 02:13:10: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:13:10: #2 alternative fragment length(s) may be 2,19 bps INFO @ Tue, 30 Jun 2020 02:13:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.20_model.r WARNING @ Tue, 30 Jun 2020 02:13:10: #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, 30 Jun 2020 02:13:10: #2 You may need to consider one of the other alternative d(s): 2,19 WARNING @ Tue, 30 Jun 2020 02:13:10: #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 02:13:10: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:13:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:13:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:13:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:13:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.05_summits.bed INFO @ Tue, 30 Jun 2020 02:13:21: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:13:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:13:46: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:13:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:13:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:13:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.10_summits.bed INFO @ Tue, 30 Jun 2020 02:13:50: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:14:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:14:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:14:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX201892/SRX201892.20_summits.bed INFO @ Tue, 30 Jun 2020 02:14:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling