Job ID = 6498284 SRX = SRX467062 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T00:09:34 prefetch.2.10.7: 1) Downloading 'SRR1164486'... 2020-06-26T00:09:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:13:43 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:13:43 prefetch.2.10.7: 1) 'SRR1164486' was downloaded successfully Read 44361476 spots for SRR1164486/SRR1164486.sra Written 44361476 spots for SRR1164486/SRR1164486.sra 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: 00:26:41 44361476 reads; of these: 44361476 (100.00%) were unpaired; of these: 1319589 (2.97%) aligned 0 times 19164646 (43.20%) aligned exactly 1 time 23877241 (53.82%) aligned >1 times 97.03% overall alignment rate Time searching: 00:26:41 Overall time: 00:26:41 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 19677927 / 43041887 = 0.4572 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 @ Fri, 26 Jun 2020 09:52:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.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, 26 Jun 2020 09:52:21: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:52:21: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:52:27: 1000000 INFO @ Fri, 26 Jun 2020 09:52:33: 2000000 INFO @ Fri, 26 Jun 2020 09:52:39: 3000000 INFO @ Fri, 26 Jun 2020 09:52:44: 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 @ Fri, 26 Jun 2020 09:52:50: 5000000 INFO @ Fri, 26 Jun 2020 09:52:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.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, 26 Jun 2020 09:52:51: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:52:51: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:52:56: 6000000 INFO @ Fri, 26 Jun 2020 09:52:57: 1000000 INFO @ Fri, 26 Jun 2020 09:53:03: 7000000 INFO @ Fri, 26 Jun 2020 09:53:04: 2000000 INFO @ Fri, 26 Jun 2020 09:53:09: 8000000 INFO @ Fri, 26 Jun 2020 09:53:11: 3000000 INFO @ Fri, 26 Jun 2020 09:53:16: 9000000 INFO @ Fri, 26 Jun 2020 09:53:17: 4000000 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 @ Fri, 26 Jun 2020 09:53:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.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, 26 Jun 2020 09:53:21: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:53:21: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:53:22: 10000000 INFO @ Fri, 26 Jun 2020 09:53:24: 5000000 INFO @ Fri, 26 Jun 2020 09:53:27: 1000000 INFO @ Fri, 26 Jun 2020 09:53:29: 11000000 INFO @ Fri, 26 Jun 2020 09:53:30: 6000000 INFO @ Fri, 26 Jun 2020 09:53:32: 2000000 INFO @ Fri, 26 Jun 2020 09:53:35: 12000000 INFO @ Fri, 26 Jun 2020 09:53:37: 7000000 INFO @ Fri, 26 Jun 2020 09:53:37: 3000000 INFO @ Fri, 26 Jun 2020 09:53:42: 13000000 INFO @ Fri, 26 Jun 2020 09:53:42: 4000000 INFO @ Fri, 26 Jun 2020 09:53:43: 8000000 INFO @ Fri, 26 Jun 2020 09:53:47: 5000000 INFO @ Fri, 26 Jun 2020 09:53:48: 14000000 INFO @ Fri, 26 Jun 2020 09:53:50: 9000000 INFO @ Fri, 26 Jun 2020 09:53:52: 6000000 INFO @ Fri, 26 Jun 2020 09:53:55: 15000000 INFO @ Fri, 26 Jun 2020 09:53:56: 10000000 INFO @ Fri, 26 Jun 2020 09:53:58: 7000000 INFO @ Fri, 26 Jun 2020 09:54:01: 16000000 INFO @ Fri, 26 Jun 2020 09:54:03: 8000000 INFO @ Fri, 26 Jun 2020 09:54:03: 11000000 INFO @ Fri, 26 Jun 2020 09:54:08: 17000000 INFO @ Fri, 26 Jun 2020 09:54:09: 9000000 INFO @ Fri, 26 Jun 2020 09:54:10: 12000000 INFO @ Fri, 26 Jun 2020 09:54:14: 18000000 INFO @ Fri, 26 Jun 2020 09:54:15: 10000000 INFO @ Fri, 26 Jun 2020 09:54:16: 13000000 INFO @ Fri, 26 Jun 2020 09:54:20: 11000000 INFO @ Fri, 26 Jun 2020 09:54:20: 19000000 INFO @ Fri, 26 Jun 2020 09:54:23: 14000000 INFO @ Fri, 26 Jun 2020 09:54:25: 12000000 INFO @ Fri, 26 Jun 2020 09:54:27: 20000000 INFO @ Fri, 26 Jun 2020 09:54:29: 15000000 INFO @ Fri, 26 Jun 2020 09:54:30: 13000000 INFO @ Fri, 26 Jun 2020 09:54:33: 21000000 INFO @ Fri, 26 Jun 2020 09:54:35: 14000000 INFO @ Fri, 26 Jun 2020 09:54:36: 16000000 INFO @ Fri, 26 Jun 2020 09:54:40: 22000000 INFO @ Fri, 26 Jun 2020 09:54:40: 15000000 INFO @ Fri, 26 Jun 2020 09:54:42: 17000000 INFO @ Fri, 26 Jun 2020 09:54:45: 16000000 INFO @ Fri, 26 Jun 2020 09:54:46: 23000000 INFO @ Fri, 26 Jun 2020 09:54:49: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:54:49: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:54:49: #1 total tags in treatment: 23363960 INFO @ Fri, 26 Jun 2020 09:54:49: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:54:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:54:49: 18000000 INFO @ Fri, 26 Jun 2020 09:54:49: #1 tags after filtering in treatment: 23363960 INFO @ Fri, 26 Jun 2020 09:54:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:54:49: #1 finished! INFO @ Fri, 26 Jun 2020 09:54:49: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:54:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:54:51: #2 number of paired peaks: 128 WARNING @ Fri, 26 Jun 2020 09:54:51: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Fri, 26 Jun 2020 09:54:51: start model_add_line... INFO @ Fri, 26 Jun 2020 09:54:51: start X-correlation... INFO @ Fri, 26 Jun 2020 09:54:51: end of X-cor INFO @ Fri, 26 Jun 2020 09:54:51: #2 finished! INFO @ Fri, 26 Jun 2020 09:54:51: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 09:54:51: #2 alternative fragment length(s) may be 2,13,16,565,598 bps INFO @ Fri, 26 Jun 2020 09:54:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.05_model.r WARNING @ Fri, 26 Jun 2020 09:54:51: #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, 26 Jun 2020 09:54:51: #2 You may need to consider one of the other alternative d(s): 2,13,16,565,598 WARNING @ Fri, 26 Jun 2020 09:54:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:54:51: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:54:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:54:51: 17000000 INFO @ Fri, 26 Jun 2020 09:54:55: 19000000 INFO @ Fri, 26 Jun 2020 09:54:57: 18000000 INFO @ Fri, 26 Jun 2020 09:55:01: 20000000 INFO @ Fri, 26 Jun 2020 09:55:02: 19000000 INFO @ Fri, 26 Jun 2020 09:55:07: 21000000 INFO @ Fri, 26 Jun 2020 09:55:07: 20000000 INFO @ Fri, 26 Jun 2020 09:55:13: 22000000 INFO @ Fri, 26 Jun 2020 09:55:13: 21000000 INFO @ Fri, 26 Jun 2020 09:55:18: 22000000 INFO @ Fri, 26 Jun 2020 09:55:18: 23000000 INFO @ Fri, 26 Jun 2020 09:55:21: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:55:21: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:55:21: #1 total tags in treatment: 23363960 INFO @ Fri, 26 Jun 2020 09:55:21: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:55:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:55:21: #1 tags after filtering in treatment: 23363960 INFO @ Fri, 26 Jun 2020 09:55:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:55:21: #1 finished! INFO @ Fri, 26 Jun 2020 09:55:21: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:55:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:55:23: #2 number of paired peaks: 128 WARNING @ Fri, 26 Jun 2020 09:55:23: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Fri, 26 Jun 2020 09:55:23: start model_add_line... INFO @ Fri, 26 Jun 2020 09:55:23: start X-correlation... INFO @ Fri, 26 Jun 2020 09:55:23: end of X-cor INFO @ Fri, 26 Jun 2020 09:55:23: #2 finished! INFO @ Fri, 26 Jun 2020 09:55:23: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 09:55:23: #2 alternative fragment length(s) may be 2,13,16,565,598 bps INFO @ Fri, 26 Jun 2020 09:55:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.10_model.r WARNING @ Fri, 26 Jun 2020 09:55:23: #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, 26 Jun 2020 09:55:23: #2 You may need to consider one of the other alternative d(s): 2,13,16,565,598 WARNING @ Fri, 26 Jun 2020 09:55:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:55:23: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:55:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:55:23: 23000000 INFO @ Fri, 26 Jun 2020 09:55:25: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 09:55:25: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 09:55:25: #1 total tags in treatment: 23363960 INFO @ Fri, 26 Jun 2020 09:55:25: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:55:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:55:26: #1 tags after filtering in treatment: 23363960 INFO @ Fri, 26 Jun 2020 09:55:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:55:26: #1 finished! INFO @ Fri, 26 Jun 2020 09:55:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:55:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:55:27: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:55:27: #2 number of paired peaks: 128 WARNING @ Fri, 26 Jun 2020 09:55:27: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Fri, 26 Jun 2020 09:55:27: start model_add_line... INFO @ Fri, 26 Jun 2020 09:55:27: start X-correlation... INFO @ Fri, 26 Jun 2020 09:55:27: end of X-cor INFO @ Fri, 26 Jun 2020 09:55:27: #2 finished! INFO @ Fri, 26 Jun 2020 09:55:27: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 09:55:27: #2 alternative fragment length(s) may be 2,13,16,565,598 bps INFO @ Fri, 26 Jun 2020 09:55:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.20_model.r WARNING @ Fri, 26 Jun 2020 09:55:27: #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, 26 Jun 2020 09:55:27: #2 You may need to consider one of the other alternative d(s): 2,13,16,565,598 WARNING @ Fri, 26 Jun 2020 09:55:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:55:27: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:55:27: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:55:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:55:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:55:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.05_summits.bed INFO @ Fri, 26 Jun 2020 09:55:45: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:55:59: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:56:03: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:56:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:56:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:56:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.10_summits.bed INFO @ Fri, 26 Jun 2020 09:56:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:56:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:56:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:56:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467062/SRX467062.20_summits.bed INFO @ Fri, 26 Jun 2020 09:56:22: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。