Job ID = 6367915 SRX = SRX4194209 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:00:08 prefetch.2.10.7: 1) Downloading 'SRR7291521'... 2020-06-16T00:00:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:00:52 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:00:52 prefetch.2.10.7: 'SRR7291521' is valid 2020-06-16T00:00:52 prefetch.2.10.7: 1) 'SRR7291521' was downloaded successfully 2020-06-16T00:00:52 prefetch.2.10.7: 'SRR7291521' has 0 unresolved dependencies Read 6127036 spots for SRR7291521/SRR7291521.sra Written 6127036 spots for SRR7291521/SRR7291521.sra 2020-06-16T00:01:27 prefetch.2.10.7: 1) Downloading 'SRR7291522'... 2020-06-16T00:01:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:02:05 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:02:06 prefetch.2.10.7: 'SRR7291522' is valid 2020-06-16T00:02:06 prefetch.2.10.7: 1) 'SRR7291522' was downloaded successfully 2020-06-16T00:02:06 prefetch.2.10.7: 'SRR7291522' has 0 unresolved dependencies Read 5986440 spots for SRR7291522/SRR7291522.sra Written 5986440 spots for SRR7291522/SRR7291522.sra 2020-06-16T00:02:41 prefetch.2.10.7: 1) Downloading 'SRR7291523'... 2020-06-16T00:02:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:03:35 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:03:35 prefetch.2.10.7: 'SRR7291523' is valid 2020-06-16T00:03:35 prefetch.2.10.7: 1) 'SRR7291523' was downloaded successfully 2020-06-16T00:03:35 prefetch.2.10.7: 'SRR7291523' has 0 unresolved dependencies Read 6132269 spots for SRR7291523/SRR7291523.sra Written 6132269 spots for SRR7291523/SRR7291523.sra 2020-06-16T00:04:07 prefetch.2.10.7: 1) Downloading 'SRR7291524'... 2020-06-16T00:04:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:05:03 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:05:04 prefetch.2.10.7: 'SRR7291524' is valid 2020-06-16T00:05:04 prefetch.2.10.7: 1) 'SRR7291524' was downloaded successfully 2020-06-16T00:05:04 prefetch.2.10.7: 'SRR7291524' has 0 unresolved dependencies Read 5930194 spots for SRR7291524/SRR7291524.sra Written 5930194 spots for SRR7291524/SRR7291524.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: 00:07:58 24175939 reads; of these: 24175939 (100.00%) were unpaired; of these: 332787 (1.38%) aligned 0 times 20138831 (83.30%) aligned exactly 1 time 3704321 (15.32%) aligned >1 times 98.62% overall alignment rate Time searching: 00:07:58 Overall time: 00:07:58 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] 3726922 / 23843152 = 0.1563 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 09:20:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.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 09:20:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:20:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:20:42: 1000000 INFO @ Tue, 16 Jun 2020 09:20:48: 2000000 INFO @ Tue, 16 Jun 2020 09:20:53: 3000000 INFO @ Tue, 16 Jun 2020 09:20:59: 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 09:21:05: 5000000 INFO @ Tue, 16 Jun 2020 09:21:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.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 09:21:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:21:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:21:11: 1000000 INFO @ Tue, 16 Jun 2020 09:21:12: 6000000 INFO @ Tue, 16 Jun 2020 09:21:17: 2000000 INFO @ Tue, 16 Jun 2020 09:21:18: 7000000 INFO @ Tue, 16 Jun 2020 09:21:22: 3000000 INFO @ Tue, 16 Jun 2020 09:21:24: 8000000 INFO @ Tue, 16 Jun 2020 09:21:27: 4000000 INFO @ Tue, 16 Jun 2020 09:21:30: 9000000 INFO @ Tue, 16 Jun 2020 09:21:33: 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 09:21:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.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 09:21:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:21:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:21:36: 10000000 INFO @ Tue, 16 Jun 2020 09:21:38: 6000000 INFO @ Tue, 16 Jun 2020 09:21:41: 1000000 INFO @ Tue, 16 Jun 2020 09:21:42: 11000000 INFO @ Tue, 16 Jun 2020 09:21:43: 7000000 INFO @ Tue, 16 Jun 2020 09:21:47: 2000000 INFO @ Tue, 16 Jun 2020 09:21:49: 12000000 INFO @ Tue, 16 Jun 2020 09:21:49: 8000000 INFO @ Tue, 16 Jun 2020 09:21:52: 3000000 INFO @ Tue, 16 Jun 2020 09:21:54: 9000000 INFO @ Tue, 16 Jun 2020 09:21:55: 13000000 INFO @ Tue, 16 Jun 2020 09:21:58: 4000000 INFO @ Tue, 16 Jun 2020 09:22:00: 10000000 INFO @ Tue, 16 Jun 2020 09:22:02: 14000000 INFO @ Tue, 16 Jun 2020 09:22:03: 5000000 INFO @ Tue, 16 Jun 2020 09:22:05: 11000000 INFO @ Tue, 16 Jun 2020 09:22:08: 15000000 INFO @ Tue, 16 Jun 2020 09:22:09: 6000000 INFO @ Tue, 16 Jun 2020 09:22:11: 12000000 INFO @ Tue, 16 Jun 2020 09:22:14: 7000000 INFO @ Tue, 16 Jun 2020 09:22:14: 16000000 INFO @ Tue, 16 Jun 2020 09:22:17: 13000000 INFO @ Tue, 16 Jun 2020 09:22:20: 8000000 INFO @ Tue, 16 Jun 2020 09:22:21: 17000000 INFO @ Tue, 16 Jun 2020 09:22:22: 14000000 INFO @ Tue, 16 Jun 2020 09:22:25: 9000000 INFO @ Tue, 16 Jun 2020 09:22:27: 18000000 INFO @ Tue, 16 Jun 2020 09:22:28: 15000000 INFO @ Tue, 16 Jun 2020 09:22:31: 10000000 INFO @ Tue, 16 Jun 2020 09:22:33: 16000000 INFO @ Tue, 16 Jun 2020 09:22:33: 19000000 INFO @ Tue, 16 Jun 2020 09:22:36: 11000000 INFO @ Tue, 16 Jun 2020 09:22:39: 17000000 INFO @ Tue, 16 Jun 2020 09:22:39: 20000000 INFO @ Tue, 16 Jun 2020 09:22:40: #1 tag size is determined as 74 bps INFO @ Tue, 16 Jun 2020 09:22:40: #1 tag size = 74 INFO @ Tue, 16 Jun 2020 09:22:40: #1 total tags in treatment: 20116230 INFO @ Tue, 16 Jun 2020 09:22:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:22:40: #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 09:22:40: #1 tags after filtering in treatment: 20116230 INFO @ Tue, 16 Jun 2020 09:22:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:22:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:22:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:22:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:22:42: 12000000 INFO @ Tue, 16 Jun 2020 09:22:42: #2 number of paired peaks: 183 WARNING @ Tue, 16 Jun 2020 09:22:42: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Tue, 16 Jun 2020 09:22:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:22:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:22:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:22:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:22:42: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:22:42: #2 alternative fragment length(s) may be 1,52,527,577 bps INFO @ Tue, 16 Jun 2020 09:22:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.05_model.r WARNING @ Tue, 16 Jun 2020 09:22:42: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:22:42: #2 You may need to consider one of the other alternative d(s): 1,52,527,577 WARNING @ Tue, 16 Jun 2020 09:22:42: #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 09:22:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:22:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:22:44: 18000000 INFO @ Tue, 16 Jun 2020 09:22:47: 13000000 INFO @ Tue, 16 Jun 2020 09:22:50: 19000000 INFO @ Tue, 16 Jun 2020 09:22:52: 14000000 INFO @ Tue, 16 Jun 2020 09:22:55: 20000000 INFO @ Tue, 16 Jun 2020 09:22:56: #1 tag size is determined as 74 bps INFO @ Tue, 16 Jun 2020 09:22:56: #1 tag size = 74 INFO @ Tue, 16 Jun 2020 09:22:56: #1 total tags in treatment: 20116230 INFO @ Tue, 16 Jun 2020 09:22:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:22:56: #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 09:22:56: #1 tags after filtering in treatment: 20116230 INFO @ Tue, 16 Jun 2020 09:22:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:22:56: #1 finished! INFO @ Tue, 16 Jun 2020 09:22:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:22:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:22:57: #2 number of paired peaks: 183 WARNING @ Tue, 16 Jun 2020 09:22:57: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Tue, 16 Jun 2020 09:22:57: start model_add_line... INFO @ Tue, 16 Jun 2020 09:22:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:22:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:22:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:22:57: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:22:57: #2 alternative fragment length(s) may be 1,52,527,577 bps INFO @ Tue, 16 Jun 2020 09:22:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.10_model.r WARNING @ Tue, 16 Jun 2020 09:22:57: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:22:57: #2 You may need to consider one of the other alternative d(s): 1,52,527,577 WARNING @ Tue, 16 Jun 2020 09:22:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:22:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:22:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:22:58: 15000000 INFO @ Tue, 16 Jun 2020 09:23:03: 16000000 INFO @ Tue, 16 Jun 2020 09:23:08: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:23:13: 18000000 INFO @ Tue, 16 Jun 2020 09:23:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:23:18: 19000000 INFO @ Tue, 16 Jun 2020 09:23:23: 20000000 INFO @ Tue, 16 Jun 2020 09:23:24: #1 tag size is determined as 74 bps INFO @ Tue, 16 Jun 2020 09:23:24: #1 tag size = 74 INFO @ Tue, 16 Jun 2020 09:23:24: #1 total tags in treatment: 20116230 INFO @ Tue, 16 Jun 2020 09:23:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:23:24: #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 09:23:24: #1 tags after filtering in treatment: 20116230 INFO @ Tue, 16 Jun 2020 09:23:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:23:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:23:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:23:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:23:26: #2 number of paired peaks: 183 WARNING @ Tue, 16 Jun 2020 09:23:26: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Tue, 16 Jun 2020 09:23:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:23:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:23:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:23:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:23:26: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 09:23:26: #2 alternative fragment length(s) may be 1,52,527,577 bps INFO @ Tue, 16 Jun 2020 09:23:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.20_model.r WARNING @ Tue, 16 Jun 2020 09:23:26: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:23:26: #2 You may need to consider one of the other alternative d(s): 1,52,527,577 WARNING @ Tue, 16 Jun 2020 09:23:26: #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 09:23:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:23:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:23:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:23:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:23:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:23:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.05_summits.bed INFO @ Tue, 16 Jun 2020 09:23:30: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (721 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:23:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:23:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:23:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.10_summits.bed INFO @ Tue, 16 Jun 2020 09:23:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (426 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:23:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:24:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:24:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:24:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194209/SRX4194209.20_summits.bed INFO @ Tue, 16 Jun 2020 09:24:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (175 records, 4 fields): 2 millis CompletedMACS2peakCalling