Job ID = 6367914 SRX = SRX4194208 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:47:14 prefetch.2.10.7: 1) Downloading 'SRR7291517'... 2020-06-15T23:47:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:48:36 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:48:36 prefetch.2.10.7: 'SRR7291517' is valid 2020-06-15T23:48:36 prefetch.2.10.7: 1) 'SRR7291517' was downloaded successfully 2020-06-15T23:48:36 prefetch.2.10.7: 'SRR7291517' has 0 unresolved dependencies Read 8141047 spots for SRR7291517/SRR7291517.sra Written 8141047 spots for SRR7291517/SRR7291517.sra 2020-06-15T23:49:16 prefetch.2.10.7: 1) Downloading 'SRR7291518'... 2020-06-15T23:49:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:50:28 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:50:28 prefetch.2.10.7: 'SRR7291518' is valid 2020-06-15T23:50:28 prefetch.2.10.7: 1) 'SRR7291518' was downloaded successfully 2020-06-15T23:50:28 prefetch.2.10.7: 'SRR7291518' has 0 unresolved dependencies Read 7979099 spots for SRR7291518/SRR7291518.sra Written 7979099 spots for SRR7291518/SRR7291518.sra 2020-06-15T23:51:08 prefetch.2.10.7: 1) Downloading 'SRR7291519'... 2020-06-15T23:51:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:52:14 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:52:15 prefetch.2.10.7: 'SRR7291519' is valid 2020-06-15T23:52:15 prefetch.2.10.7: 1) 'SRR7291519' was downloaded successfully 2020-06-15T23:52:15 prefetch.2.10.7: 'SRR7291519' has 0 unresolved dependencies Read 8129009 spots for SRR7291519/SRR7291519.sra Written 8129009 spots for SRR7291519/SRR7291519.sra 2020-06-15T23:52:56 prefetch.2.10.7: 1) Downloading 'SRR7291520'... 2020-06-15T23:52:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:54:11 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:54:11 prefetch.2.10.7: 'SRR7291520' is valid 2020-06-15T23:54:11 prefetch.2.10.7: 1) 'SRR7291520' was downloaded successfully 2020-06-15T23:54:11 prefetch.2.10.7: 'SRR7291520' has 0 unresolved dependencies Read 7895317 spots for SRR7291520/SRR7291520.sra Written 7895317 spots for SRR7291520/SRR7291520.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:51 32144472 reads; of these: 32144472 (100.00%) were unpaired; of these: 491855 (1.53%) aligned 0 times 26715052 (83.11%) aligned exactly 1 time 4937565 (15.36%) aligned >1 times 98.47% overall alignment rate Time searching: 00:11:52 Overall time: 00:11:52 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] 5731545 / 31652617 = 0.1811 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 09:16:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.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 09:16:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:16:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:16:40: 1000000 INFO @ Tue, 16 Jun 2020 09:16:46: 2000000 INFO @ Tue, 16 Jun 2020 09:16:53: 3000000 INFO @ Tue, 16 Jun 2020 09:17:00: 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 09:17:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.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 09:17:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:17:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:17:08: 5000000 INFO @ Tue, 16 Jun 2020 09:17:12: 1000000 INFO @ Tue, 16 Jun 2020 09:17:16: 6000000 INFO @ Tue, 16 Jun 2020 09:17:21: 2000000 INFO @ Tue, 16 Jun 2020 09:17:25: 7000000 INFO @ Tue, 16 Jun 2020 09:17:31: 3000000 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 09:17:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.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 09:17:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:17:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:17:33: 8000000 INFO @ Tue, 16 Jun 2020 09:17:40: 4000000 INFO @ Tue, 16 Jun 2020 09:17:42: 9000000 INFO @ Tue, 16 Jun 2020 09:17:43: 1000000 INFO @ Tue, 16 Jun 2020 09:17:50: 5000000 INFO @ Tue, 16 Jun 2020 09:17:51: 10000000 INFO @ Tue, 16 Jun 2020 09:17:52: 2000000 INFO @ Tue, 16 Jun 2020 09:17:59: 6000000 INFO @ Tue, 16 Jun 2020 09:18:00: 11000000 INFO @ Tue, 16 Jun 2020 09:18:02: 3000000 INFO @ Tue, 16 Jun 2020 09:18:09: 7000000 INFO @ Tue, 16 Jun 2020 09:18:09: 12000000 INFO @ Tue, 16 Jun 2020 09:18:12: 4000000 INFO @ Tue, 16 Jun 2020 09:18:17: 13000000 INFO @ Tue, 16 Jun 2020 09:18:18: 8000000 INFO @ Tue, 16 Jun 2020 09:18:22: 5000000 INFO @ Tue, 16 Jun 2020 09:18:26: 14000000 INFO @ Tue, 16 Jun 2020 09:18:27: 9000000 INFO @ Tue, 16 Jun 2020 09:18:31: 6000000 INFO @ Tue, 16 Jun 2020 09:18:35: 15000000 INFO @ Tue, 16 Jun 2020 09:18:36: 10000000 INFO @ Tue, 16 Jun 2020 09:18:40: 7000000 INFO @ Tue, 16 Jun 2020 09:18:43: 16000000 INFO @ Tue, 16 Jun 2020 09:18:46: 11000000 INFO @ Tue, 16 Jun 2020 09:18:49: 8000000 INFO @ Tue, 16 Jun 2020 09:18:52: 17000000 INFO @ Tue, 16 Jun 2020 09:18:55: 12000000 INFO @ Tue, 16 Jun 2020 09:18:59: 9000000 INFO @ Tue, 16 Jun 2020 09:19:00: 18000000 INFO @ Tue, 16 Jun 2020 09:19:04: 13000000 INFO @ Tue, 16 Jun 2020 09:19:08: 10000000 INFO @ Tue, 16 Jun 2020 09:19:09: 19000000 INFO @ Tue, 16 Jun 2020 09:19:14: 14000000 INFO @ Tue, 16 Jun 2020 09:19:17: 20000000 INFO @ Tue, 16 Jun 2020 09:19:18: 11000000 INFO @ Tue, 16 Jun 2020 09:19:23: 15000000 INFO @ Tue, 16 Jun 2020 09:19:26: 21000000 INFO @ Tue, 16 Jun 2020 09:19:27: 12000000 INFO @ Tue, 16 Jun 2020 09:19:32: 16000000 INFO @ Tue, 16 Jun 2020 09:19:35: 22000000 INFO @ Tue, 16 Jun 2020 09:19:37: 13000000 INFO @ Tue, 16 Jun 2020 09:19:42: 17000000 INFO @ Tue, 16 Jun 2020 09:19:44: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:19:46: 14000000 INFO @ Tue, 16 Jun 2020 09:19:51: 18000000 INFO @ Tue, 16 Jun 2020 09:19:53: 24000000 INFO @ Tue, 16 Jun 2020 09:19:56: 15000000 INFO @ Tue, 16 Jun 2020 09:20:00: 19000000 INFO @ Tue, 16 Jun 2020 09:20:01: 25000000 INFO @ Tue, 16 Jun 2020 09:20:05: 16000000 INFO @ Tue, 16 Jun 2020 09:20:09: #1 tag size is determined as 69 bps INFO @ Tue, 16 Jun 2020 09:20:09: #1 tag size = 69 INFO @ Tue, 16 Jun 2020 09:20:09: #1 total tags in treatment: 25921072 INFO @ Tue, 16 Jun 2020 09:20:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:09: #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 09:20:10: 20000000 INFO @ Tue, 16 Jun 2020 09:20:10: #1 tags after filtering in treatment: 25921072 INFO @ Tue, 16 Jun 2020 09:20:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:12: #2 number of paired peaks: 118 WARNING @ Tue, 16 Jun 2020 09:20:12: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:12: #2 predicted fragment length is 60 bps INFO @ Tue, 16 Jun 2020 09:20:12: #2 alternative fragment length(s) may be 1,60,529 bps INFO @ Tue, 16 Jun 2020 09:20:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.05_model.r WARNING @ Tue, 16 Jun 2020 09:20:12: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:12: #2 You may need to consider one of the other alternative d(s): 1,60,529 WARNING @ Tue, 16 Jun 2020 09:20:12: #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 09:20:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:14: 17000000 INFO @ Tue, 16 Jun 2020 09:20:19: 21000000 INFO @ Tue, 16 Jun 2020 09:20:23: 18000000 INFO @ Tue, 16 Jun 2020 09:20:28: 22000000 INFO @ Tue, 16 Jun 2020 09:20:32: 19000000 INFO @ Tue, 16 Jun 2020 09:20:38: 23000000 INFO @ Tue, 16 Jun 2020 09:20:41: 20000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:20:47: 24000000 INFO @ Tue, 16 Jun 2020 09:20:50: 21000000 INFO @ Tue, 16 Jun 2020 09:20:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:55: 25000000 INFO @ Tue, 16 Jun 2020 09:20:59: 22000000 INFO @ Tue, 16 Jun 2020 09:21:03: #1 tag size is determined as 69 bps INFO @ Tue, 16 Jun 2020 09:21:03: #1 tag size = 69 INFO @ Tue, 16 Jun 2020 09:21:03: #1 total tags in treatment: 25921072 INFO @ Tue, 16 Jun 2020 09:21:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:03: #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 09:21:03: #1 tags after filtering in treatment: 25921072 INFO @ Tue, 16 Jun 2020 09:21:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:05: #2 number of paired peaks: 118 WARNING @ Tue, 16 Jun 2020 09:21:05: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:05: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:05: #2 predicted fragment length is 60 bps INFO @ Tue, 16 Jun 2020 09:21:05: #2 alternative fragment length(s) may be 1,60,529 bps INFO @ Tue, 16 Jun 2020 09:21:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.10_model.r WARNING @ Tue, 16 Jun 2020 09:21:05: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:05: #2 You may need to consider one of the other alternative d(s): 1,60,529 WARNING @ Tue, 16 Jun 2020 09:21:05: #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 09:21:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:07: 23000000 INFO @ Tue, 16 Jun 2020 09:21:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.05_summits.bed INFO @ Tue, 16 Jun 2020 09:21:14: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (710 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:21:15: 24000000 INFO @ Tue, 16 Jun 2020 09:21:23: 25000000 INFO @ Tue, 16 Jun 2020 09:21:30: #1 tag size is determined as 69 bps INFO @ Tue, 16 Jun 2020 09:21:30: #1 tag size = 69 INFO @ Tue, 16 Jun 2020 09:21:30: #1 total tags in treatment: 25921072 INFO @ Tue, 16 Jun 2020 09:21:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:30: #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 09:21:30: #1 tags after filtering in treatment: 25921072 INFO @ Tue, 16 Jun 2020 09:21:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:30: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:32: #2 number of paired peaks: 118 WARNING @ Tue, 16 Jun 2020 09:21:32: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:32: #2 predicted fragment length is 60 bps INFO @ Tue, 16 Jun 2020 09:21:32: #2 alternative fragment length(s) may be 1,60,529 bps INFO @ Tue, 16 Jun 2020 09:21:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.20_model.r WARNING @ Tue, 16 Jun 2020 09:21:32: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:32: #2 You may need to consider one of the other alternative d(s): 1,60,529 WARNING @ Tue, 16 Jun 2020 09:21:32: #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 09:21:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:22:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:22:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:22:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.10_summits.bed INFO @ Tue, 16 Jun 2020 09:22:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (459 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:22:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:22:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:22:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:22:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194208/SRX4194208.20_summits.bed INFO @ Tue, 16 Jun 2020 09:22:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (191 records, 4 fields): 1 millis CompletedMACS2peakCalling