Job ID = 6368606 SRX = SRX5020831 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:27:16 prefetch.2.10.7: 1) Downloading 'SRR8201454'... 2020-06-16T00:27:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:30:17 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:30:18 prefetch.2.10.7: 'SRR8201454' is valid 2020-06-16T00:30:18 prefetch.2.10.7: 1) 'SRR8201454' was downloaded successfully 2020-06-16T00:30:18 prefetch.2.10.7: 'SRR8201454' has 0 unresolved dependencies Read 24411962 spots for SRR8201454/SRR8201454.sra Written 24411962 spots for SRR8201454/SRR8201454.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: 00:05:19 24411962 reads; of these: 24411962 (100.00%) were unpaired; of these: 642570 (2.63%) aligned 0 times 19812926 (81.16%) aligned exactly 1 time 3956466 (16.21%) aligned >1 times 97.37% overall alignment rate Time searching: 00:05:19 Overall time: 00:05:19 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 12 files... [bam_rmdupse_core] 2696205 / 23769392 = 0.1134 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 09:42:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.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 09:42:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:42:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:40: 1000000 INFO @ Tue, 16 Jun 2020 09:42:45: 2000000 INFO @ Tue, 16 Jun 2020 09:42:50: 3000000 INFO @ Tue, 16 Jun 2020 09:42:55: 4000000 INFO @ Tue, 16 Jun 2020 09:43:01: 5000000 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 09:43:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.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 09:43:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:43:06: 6000000 INFO @ Tue, 16 Jun 2020 09:43:09: 1000000 INFO @ Tue, 16 Jun 2020 09:43:12: 7000000 INFO @ Tue, 16 Jun 2020 09:43:15: 2000000 INFO @ Tue, 16 Jun 2020 09:43:17: 8000000 INFO @ Tue, 16 Jun 2020 09:43:20: 3000000 INFO @ Tue, 16 Jun 2020 09:43:23: 9000000 INFO @ Tue, 16 Jun 2020 09:43:26: 4000000 INFO @ Tue, 16 Jun 2020 09:43:29: 10000000 INFO @ Tue, 16 Jun 2020 09:43:32: 5000000 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 09:43:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.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 09:43:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:43:34: 11000000 INFO @ Tue, 16 Jun 2020 09:43:38: 6000000 INFO @ Tue, 16 Jun 2020 09:43:40: 12000000 INFO @ Tue, 16 Jun 2020 09:43:41: 1000000 INFO @ Tue, 16 Jun 2020 09:43:44: 7000000 INFO @ Tue, 16 Jun 2020 09:43:46: 13000000 INFO @ Tue, 16 Jun 2020 09:43:48: 2000000 INFO @ Tue, 16 Jun 2020 09:43:50: 8000000 INFO @ Tue, 16 Jun 2020 09:43:52: 14000000 INFO @ Tue, 16 Jun 2020 09:43:55: 3000000 INFO @ Tue, 16 Jun 2020 09:43:56: 9000000 INFO @ Tue, 16 Jun 2020 09:43:58: 15000000 INFO @ Tue, 16 Jun 2020 09:44:02: 4000000 INFO @ Tue, 16 Jun 2020 09:44:02: 10000000 INFO @ Tue, 16 Jun 2020 09:44:04: 16000000 INFO @ Tue, 16 Jun 2020 09:44:08: 11000000 INFO @ Tue, 16 Jun 2020 09:44:08: 5000000 INFO @ Tue, 16 Jun 2020 09:44:10: 17000000 INFO @ Tue, 16 Jun 2020 09:44:14: 12000000 INFO @ Tue, 16 Jun 2020 09:44:15: 6000000 INFO @ Tue, 16 Jun 2020 09:44:16: 18000000 INFO @ Tue, 16 Jun 2020 09:44:20: 13000000 INFO @ Tue, 16 Jun 2020 09:44:22: 7000000 INFO @ Tue, 16 Jun 2020 09:44:22: 19000000 INFO @ Tue, 16 Jun 2020 09:44:26: 14000000 INFO @ Tue, 16 Jun 2020 09:44:28: 20000000 INFO @ Tue, 16 Jun 2020 09:44:29: 8000000 INFO @ Tue, 16 Jun 2020 09:44:32: 15000000 INFO @ Tue, 16 Jun 2020 09:44:34: 21000000 INFO @ Tue, 16 Jun 2020 09:44:35: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:44:35: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:44:35: #1 total tags in treatment: 21073187 INFO @ Tue, 16 Jun 2020 09:44:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:35: #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 09:44:35: #1 tags after filtering in treatment: 21073187 INFO @ Tue, 16 Jun 2020 09:44:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:44:35: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:44:35: 9000000 INFO @ Tue, 16 Jun 2020 09:44:37: #2 number of paired peaks: 178 WARNING @ Tue, 16 Jun 2020 09:44:37: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Tue, 16 Jun 2020 09:44:37: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:37: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:37: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:37: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:37: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:44:37: #2 alternative fragment length(s) may be 1,21,531,547,563,589 bps INFO @ Tue, 16 Jun 2020 09:44:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.05_model.r WARNING @ Tue, 16 Jun 2020 09:44:37: #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 09:44:37: #2 You may need to consider one of the other alternative d(s): 1,21,531,547,563,589 WARNING @ Tue, 16 Jun 2020 09:44:37: #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 09:44:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:44:38: 16000000 INFO @ Tue, 16 Jun 2020 09:44:42: 10000000 INFO @ Tue, 16 Jun 2020 09:44:44: 17000000 INFO @ Tue, 16 Jun 2020 09:44:49: 11000000 INFO @ Tue, 16 Jun 2020 09:44:50: 18000000 INFO @ Tue, 16 Jun 2020 09:44:56: 19000000 INFO @ Tue, 16 Jun 2020 09:44:56: 12000000 INFO @ Tue, 16 Jun 2020 09:45:01: 20000000 INFO @ Tue, 16 Jun 2020 09:45:03: 13000000 INFO @ Tue, 16 Jun 2020 09:45:07: 21000000 INFO @ Tue, 16 Jun 2020 09:45:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:45:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:45:08: #1 total tags in treatment: 21073187 INFO @ Tue, 16 Jun 2020 09:45:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:08: #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 09:45:08: #1 tags after filtering in treatment: 21073187 INFO @ Tue, 16 Jun 2020 09:45:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:45:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:09: 14000000 INFO @ Tue, 16 Jun 2020 09:45:10: #2 number of paired peaks: 178 WARNING @ Tue, 16 Jun 2020 09:45:10: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Tue, 16 Jun 2020 09:45:10: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:10: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:10: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:10: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:10: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:45:10: #2 alternative fragment length(s) may be 1,21,531,547,563,589 bps INFO @ Tue, 16 Jun 2020 09:45:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.10_model.r WARNING @ Tue, 16 Jun 2020 09:45:10: #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 09:45:10: #2 You may need to consider one of the other alternative d(s): 1,21,531,547,563,589 WARNING @ Tue, 16 Jun 2020 09:45:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:45:10: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:45:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:45:16: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:45:22: 16000000 INFO @ Tue, 16 Jun 2020 09:45:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:45:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:45:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.05_summits.bed INFO @ Tue, 16 Jun 2020 09:45:27: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:45:29: 17000000 INFO @ Tue, 16 Jun 2020 09:45:35: 18000000 INFO @ Tue, 16 Jun 2020 09:45:41: 19000000 INFO @ Tue, 16 Jun 2020 09:45:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:45:47: 20000000 INFO @ Tue, 16 Jun 2020 09:45:54: 21000000 INFO @ Tue, 16 Jun 2020 09:45:54: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:45:54: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:45:54: #1 total tags in treatment: 21073187 INFO @ Tue, 16 Jun 2020 09:45:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:45:54: #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 09:45:54: #1 tags after filtering in treatment: 21073187 INFO @ Tue, 16 Jun 2020 09:45:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:45:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:45:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:45:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:45:56: #2 number of paired peaks: 178 WARNING @ Tue, 16 Jun 2020 09:45:56: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Tue, 16 Jun 2020 09:45:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:45:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:45:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:45:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:45:56: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:45:56: #2 alternative fragment length(s) may be 1,21,531,547,563,589 bps INFO @ Tue, 16 Jun 2020 09:45:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.20_model.r WARNING @ Tue, 16 Jun 2020 09:45:56: #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 09:45:56: #2 You may need to consider one of the other alternative d(s): 1,21,531,547,563,589 WARNING @ Tue, 16 Jun 2020 09:45:56: #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 09:45:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:45:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:45:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:45:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:45:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.10_summits.bed INFO @ Tue, 16 Jun 2020 09:45:58: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:46:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:46:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:46:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:46:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020831/SRX5020831.20_summits.bed INFO @ Tue, 16 Jun 2020 09:46:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling