Job ID = 6368877 SRX = SRX6619574 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:47:39 prefetch.2.10.7: 1) Downloading 'SRR9866035'... 2020-06-16T00:47:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:50:44 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:50:44 prefetch.2.10.7: 1) 'SRR9866035' was downloaded successfully 2020-06-16T00:50:44 prefetch.2.10.7: 'SRR9866035' has 0 unresolved dependencies Read 32861226 spots for SRR9866035/SRR9866035.sra Written 32861226 spots for SRR9866035/SRR9866035.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: 00:07:36 32861226 reads; of these: 32861226 (100.00%) were unpaired; of these: 2438004 (7.42%) aligned 0 times 25632105 (78.00%) aligned exactly 1 time 4791117 (14.58%) aligned >1 times 92.58% overall alignment rate Time searching: 00:07:36 Overall time: 00:07:36 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 5356850 / 30423222 = 0.1761 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, 16 Jun 2020 10:09:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 16 Jun 2020 10:09:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:09:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:09:43: 1000000 INFO @ Tue, 16 Jun 2020 10:09:49: 2000000 INFO @ Tue, 16 Jun 2020 10:09:55: 3000000 INFO @ Tue, 16 Jun 2020 10:10:01: 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, 16 Jun 2020 10:10:07: 5000000 INFO @ Tue, 16 Jun 2020 10:10:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 16 Jun 2020 10:10:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:10:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:10:13: 6000000 INFO @ Tue, 16 Jun 2020 10:10:15: 1000000 INFO @ Tue, 16 Jun 2020 10:10:19: 7000000 INFO @ Tue, 16 Jun 2020 10:10:22: 2000000 INFO @ Tue, 16 Jun 2020 10:10:25: 8000000 INFO @ Tue, 16 Jun 2020 10:10:29: 3000000 INFO @ Tue, 16 Jun 2020 10:10:31: 9000000 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, 16 Jun 2020 10:10:36: 4000000 INFO @ Tue, 16 Jun 2020 10:10:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 16 Jun 2020 10:10:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:10:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:10:37: 10000000 INFO @ Tue, 16 Jun 2020 10:10:44: 5000000 INFO @ Tue, 16 Jun 2020 10:10:44: 11000000 INFO @ Tue, 16 Jun 2020 10:10:44: 1000000 INFO @ Tue, 16 Jun 2020 10:10:50: 12000000 INFO @ Tue, 16 Jun 2020 10:10:50: 2000000 INFO @ Tue, 16 Jun 2020 10:10:51: 6000000 INFO @ Tue, 16 Jun 2020 10:10:57: 3000000 INFO @ Tue, 16 Jun 2020 10:10:57: 13000000 INFO @ Tue, 16 Jun 2020 10:10:59: 7000000 INFO @ Tue, 16 Jun 2020 10:11:04: 4000000 INFO @ Tue, 16 Jun 2020 10:11:04: 14000000 INFO @ Tue, 16 Jun 2020 10:11:08: 8000000 INFO @ Tue, 16 Jun 2020 10:11:10: 15000000 INFO @ Tue, 16 Jun 2020 10:11:11: 5000000 INFO @ Tue, 16 Jun 2020 10:11:16: 9000000 INFO @ Tue, 16 Jun 2020 10:11:18: 16000000 INFO @ Tue, 16 Jun 2020 10:11:19: 6000000 INFO @ Tue, 16 Jun 2020 10:11:25: 10000000 INFO @ Tue, 16 Jun 2020 10:11:26: 17000000 INFO @ Tue, 16 Jun 2020 10:11:27: 7000000 INFO @ Tue, 16 Jun 2020 10:11:34: 18000000 INFO @ Tue, 16 Jun 2020 10:11:35: 11000000 INFO @ Tue, 16 Jun 2020 10:11:35: 8000000 INFO @ Tue, 16 Jun 2020 10:11:42: 19000000 INFO @ Tue, 16 Jun 2020 10:11:43: 9000000 INFO @ Tue, 16 Jun 2020 10:11:45: 12000000 INFO @ Tue, 16 Jun 2020 10:11:50: 20000000 INFO @ Tue, 16 Jun 2020 10:11:52: 10000000 INFO @ Tue, 16 Jun 2020 10:11:53: 13000000 INFO @ Tue, 16 Jun 2020 10:11:59: 21000000 INFO @ Tue, 16 Jun 2020 10:12:01: 11000000 INFO @ Tue, 16 Jun 2020 10:12:03: 14000000 INFO @ Tue, 16 Jun 2020 10:12:06: 22000000 INFO @ Tue, 16 Jun 2020 10:12:10: 12000000 INFO @ Tue, 16 Jun 2020 10:12:12: 15000000 INFO @ Tue, 16 Jun 2020 10:12:15: 23000000 INFO @ Tue, 16 Jun 2020 10:12:18: 13000000 INFO @ Tue, 16 Jun 2020 10:12:21: 16000000 INFO @ Tue, 16 Jun 2020 10:12:22: 24000000 INFO @ Tue, 16 Jun 2020 10:12:26: 14000000 INFO @ Tue, 16 Jun 2020 10:12:30: 25000000 INFO @ Tue, 16 Jun 2020 10:12:30: 17000000 INFO @ Tue, 16 Jun 2020 10:12:30: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:12:30: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:12:30: #1 total tags in treatment: 25066372 INFO @ Tue, 16 Jun 2020 10:12:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:12:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 10:12:31: #1 tags after filtering in treatment: 25066372 INFO @ Tue, 16 Jun 2020 10:12:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:12:31: #1 finished! INFO @ Tue, 16 Jun 2020 10:12:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:12:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:12:33: #2 number of paired peaks: 143 WARNING @ Tue, 16 Jun 2020 10:12:33: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Tue, 16 Jun 2020 10:12:33: start model_add_line... INFO @ Tue, 16 Jun 2020 10:12:33: start X-correlation... INFO @ Tue, 16 Jun 2020 10:12:33: end of X-cor INFO @ Tue, 16 Jun 2020 10:12:33: #2 finished! INFO @ Tue, 16 Jun 2020 10:12:33: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:12:33: #2 alternative fragment length(s) may be 1,43,564,589 bps INFO @ Tue, 16 Jun 2020 10:12:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.05_model.r WARNING @ Tue, 16 Jun 2020 10:12:33: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:12:33: #2 You may need to consider one of the other alternative d(s): 1,43,564,589 WARNING @ Tue, 16 Jun 2020 10:12:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 10:12:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:12:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:12:34: 15000000 INFO @ Tue, 16 Jun 2020 10:12:38: 18000000 INFO @ Tue, 16 Jun 2020 10:12:41: 16000000 INFO @ Tue, 16 Jun 2020 10:12:46: 19000000 INFO @ Tue, 16 Jun 2020 10:12:48: 17000000 INFO @ Tue, 16 Jun 2020 10:12:53: 20000000 INFO @ Tue, 16 Jun 2020 10:12:55: 18000000 INFO @ Tue, 16 Jun 2020 10:13:01: 21000000 INFO @ Tue, 16 Jun 2020 10:13:02: 19000000 INFO @ Tue, 16 Jun 2020 10:13:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:13:09: 20000000 INFO @ Tue, 16 Jun 2020 10:13:09: 22000000 INFO @ Tue, 16 Jun 2020 10:13:15: 21000000 INFO @ Tue, 16 Jun 2020 10:13:17: 23000000 INFO @ Tue, 16 Jun 2020 10:13:22: 22000000 INFO @ Tue, 16 Jun 2020 10:13:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:13:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:13:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.05_summits.bed INFO @ Tue, 16 Jun 2020 10:13:23: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:13:24: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:13:29: 23000000 INFO @ Tue, 16 Jun 2020 10:13:32: 25000000 INFO @ Tue, 16 Jun 2020 10:13:33: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:13:33: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:13:33: #1 total tags in treatment: 25066372 INFO @ Tue, 16 Jun 2020 10:13:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:13:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 10:13:33: #1 tags after filtering in treatment: 25066372 INFO @ Tue, 16 Jun 2020 10:13:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:13:33: #1 finished! INFO @ Tue, 16 Jun 2020 10:13:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:13:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:13:35: #2 number of paired peaks: 143 WARNING @ Tue, 16 Jun 2020 10:13:35: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Tue, 16 Jun 2020 10:13:35: start model_add_line... INFO @ Tue, 16 Jun 2020 10:13:35: start X-correlation... INFO @ Tue, 16 Jun 2020 10:13:35: end of X-cor INFO @ Tue, 16 Jun 2020 10:13:35: #2 finished! INFO @ Tue, 16 Jun 2020 10:13:35: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:13:35: #2 alternative fragment length(s) may be 1,43,564,589 bps INFO @ Tue, 16 Jun 2020 10:13:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.10_model.r WARNING @ Tue, 16 Jun 2020 10:13:35: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:13:35: #2 You may need to consider one of the other alternative d(s): 1,43,564,589 WARNING @ Tue, 16 Jun 2020 10:13:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 10:13:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:13:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:13:36: 24000000 INFO @ Tue, 16 Jun 2020 10:13:43: 25000000 INFO @ Tue, 16 Jun 2020 10:13:43: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:13:43: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:13:43: #1 total tags in treatment: 25066372 INFO @ Tue, 16 Jun 2020 10:13:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:13:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 10:13:44: #1 tags after filtering in treatment: 25066372 INFO @ Tue, 16 Jun 2020 10:13:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 10:13:44: #1 finished! INFO @ Tue, 16 Jun 2020 10:13:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:13:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:13:45: #2 number of paired peaks: 143 WARNING @ Tue, 16 Jun 2020 10:13:45: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Tue, 16 Jun 2020 10:13:45: start model_add_line... INFO @ Tue, 16 Jun 2020 10:13:46: start X-correlation... INFO @ Tue, 16 Jun 2020 10:13:46: end of X-cor INFO @ Tue, 16 Jun 2020 10:13:46: #2 finished! INFO @ Tue, 16 Jun 2020 10:13:46: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 10:13:46: #2 alternative fragment length(s) may be 1,43,564,589 bps INFO @ Tue, 16 Jun 2020 10:13:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.20_model.r WARNING @ Tue, 16 Jun 2020 10:13:46: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 10:13:46: #2 You may need to consider one of the other alternative d(s): 1,43,564,589 WARNING @ Tue, 16 Jun 2020 10:13:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 10:13:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:13:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:14:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:14:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:14:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:14:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:14:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.10_summits.bed INFO @ Tue, 16 Jun 2020 10:14:26: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:14:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:14:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:14:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6619574/SRX6619574.20_summits.bed INFO @ Tue, 16 Jun 2020 10:14:36: 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。