Job ID = 6367917 SRX = SRX4194211 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:43:44 prefetch.2.10.7: 1) Downloading 'SRR7291530'... 2020-06-15T23:43:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:45:21 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:45:21 prefetch.2.10.7: 'SRR7291530' is valid 2020-06-15T23:45:21 prefetch.2.10.7: 1) 'SRR7291530' was downloaded successfully 2020-06-15T23:45:21 prefetch.2.10.7: 'SRR7291530' has 0 unresolved dependencies Read 7161842 spots for SRR7291530/SRR7291530.sra Written 7161842 spots for SRR7291530/SRR7291530.sra 2020-06-15T23:45:59 prefetch.2.10.7: 1) Downloading 'SRR7291531'... 2020-06-15T23:45:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:15 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:16 prefetch.2.10.7: 'SRR7291531' is valid 2020-06-15T23:47:16 prefetch.2.10.7: 1) 'SRR7291531' was downloaded successfully 2020-06-15T23:47:16 prefetch.2.10.7: 'SRR7291531' has 0 unresolved dependencies Read 6982891 spots for SRR7291531/SRR7291531.sra Written 6982891 spots for SRR7291531/SRR7291531.sra 2020-06-15T23:47:54 prefetch.2.10.7: 1) Downloading 'SRR7291532'... 2020-06-15T23:47:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:04 prefetch.2.10.7: 'SRR7291532' is valid 2020-06-15T23:49:04 prefetch.2.10.7: 1) 'SRR7291532' was downloaded successfully 2020-06-15T23:49:04 prefetch.2.10.7: 'SRR7291532' has 0 unresolved dependencies Read 7161453 spots for SRR7291532/SRR7291532.sra Written 7161453 spots for SRR7291532/SRR7291532.sra 2020-06-15T23:49:41 prefetch.2.10.7: 1) Downloading 'SRR7291533'... 2020-06-15T23:49:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:50:37 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:50:38 prefetch.2.10.7: 'SRR7291533' is valid 2020-06-15T23:50:38 prefetch.2.10.7: 1) 'SRR7291533' was downloaded successfully 2020-06-15T23:50:38 prefetch.2.10.7: 'SRR7291533' has 0 unresolved dependencies Read 6924975 spots for SRR7291533/SRR7291533.sra Written 6924975 spots for SRR7291533/SRR7291533.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: 00:10:39 28231161 reads; of these: 28231161 (100.00%) were unpaired; of these: 840177 (2.98%) aligned 0 times 23011713 (81.51%) aligned exactly 1 time 4379271 (15.51%) aligned >1 times 97.02% overall alignment rate Time searching: 00:10:40 Overall time: 00:10:40 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] 4392498 / 27390984 = 0.1604 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 09:10:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.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 09:10:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:50: 1000000 INFO @ Tue, 16 Jun 2020 09:10:56: 2000000 INFO @ Tue, 16 Jun 2020 09:11:03: 3000000 INFO @ Tue, 16 Jun 2020 09:11:09: 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 09:11:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.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 09:11:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:16: 5000000 INFO @ Tue, 16 Jun 2020 09:11:21: 1000000 INFO @ Tue, 16 Jun 2020 09:11:23: 6000000 INFO @ Tue, 16 Jun 2020 09:11:28: 2000000 INFO @ Tue, 16 Jun 2020 09:11:30: 7000000 INFO @ Tue, 16 Jun 2020 09:11:35: 3000000 INFO @ Tue, 16 Jun 2020 09:11:38: 8000000 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 09:11:42: 4000000 INFO @ Tue, 16 Jun 2020 09:11:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.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 09:11:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:45: 9000000 INFO @ Tue, 16 Jun 2020 09:11:50: 5000000 INFO @ Tue, 16 Jun 2020 09:11:52: 1000000 INFO @ Tue, 16 Jun 2020 09:11:53: 10000000 INFO @ Tue, 16 Jun 2020 09:11:58: 6000000 INFO @ Tue, 16 Jun 2020 09:12:01: 11000000 INFO @ Tue, 16 Jun 2020 09:12:01: 2000000 INFO @ Tue, 16 Jun 2020 09:12:06: 7000000 INFO @ Tue, 16 Jun 2020 09:12:09: 12000000 INFO @ Tue, 16 Jun 2020 09:12:10: 3000000 INFO @ Tue, 16 Jun 2020 09:12:14: 8000000 INFO @ Tue, 16 Jun 2020 09:12:17: 13000000 INFO @ Tue, 16 Jun 2020 09:12:18: 4000000 INFO @ Tue, 16 Jun 2020 09:12:21: 9000000 INFO @ Tue, 16 Jun 2020 09:12:24: 14000000 INFO @ Tue, 16 Jun 2020 09:12:27: 5000000 INFO @ Tue, 16 Jun 2020 09:12:29: 10000000 INFO @ Tue, 16 Jun 2020 09:12:32: 15000000 INFO @ Tue, 16 Jun 2020 09:12:36: 6000000 INFO @ Tue, 16 Jun 2020 09:12:37: 11000000 INFO @ Tue, 16 Jun 2020 09:12:41: 16000000 INFO @ Tue, 16 Jun 2020 09:12:44: 7000000 INFO @ Tue, 16 Jun 2020 09:12:45: 12000000 INFO @ Tue, 16 Jun 2020 09:12:49: 17000000 INFO @ Tue, 16 Jun 2020 09:12:53: 8000000 INFO @ Tue, 16 Jun 2020 09:12:53: 13000000 INFO @ Tue, 16 Jun 2020 09:12:57: 18000000 INFO @ Tue, 16 Jun 2020 09:13:01: 14000000 INFO @ Tue, 16 Jun 2020 09:13:01: 9000000 INFO @ Tue, 16 Jun 2020 09:13:06: 19000000 INFO @ Tue, 16 Jun 2020 09:13:09: 15000000 INFO @ Tue, 16 Jun 2020 09:13:10: 10000000 INFO @ Tue, 16 Jun 2020 09:13:14: 20000000 INFO @ Tue, 16 Jun 2020 09:13:17: 16000000 INFO @ Tue, 16 Jun 2020 09:13:18: 11000000 INFO @ Tue, 16 Jun 2020 09:13:22: 21000000 INFO @ Tue, 16 Jun 2020 09:13:26: 17000000 INFO @ Tue, 16 Jun 2020 09:13:27: 12000000 INFO @ Tue, 16 Jun 2020 09:13:31: 22000000 INFO @ Tue, 16 Jun 2020 09:13:34: 18000000 INFO @ Tue, 16 Jun 2020 09:13:36: 13000000 INFO @ Tue, 16 Jun 2020 09:13:40: #1 tag size is determined as 64 bps INFO @ Tue, 16 Jun 2020 09:13:40: #1 tag size = 64 INFO @ Tue, 16 Jun 2020 09:13:40: #1 total tags in treatment: 22998486 INFO @ Tue, 16 Jun 2020 09:13:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:40: #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 09:13:40: #1 tags after filtering in treatment: 22998486 INFO @ Tue, 16 Jun 2020 09:13:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:13:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:40: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:13:42: #2 number of paired peaks: 158 WARNING @ Tue, 16 Jun 2020 09:13:42: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 16 Jun 2020 09:13:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:42: #2 predicted fragment length is 58 bps INFO @ Tue, 16 Jun 2020 09:13:42: #2 alternative fragment length(s) may be 2,58,577 bps INFO @ Tue, 16 Jun 2020 09:13:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.05_model.r WARNING @ Tue, 16 Jun 2020 09:13:42: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:13:42: #2 You may need to consider one of the other alternative d(s): 2,58,577 WARNING @ Tue, 16 Jun 2020 09:13:42: #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 09:13:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:42: 19000000 INFO @ Tue, 16 Jun 2020 09:13:45: 14000000 INFO @ Tue, 16 Jun 2020 09:13:51: 20000000 INFO @ Tue, 16 Jun 2020 09:13:54: 15000000 INFO @ Tue, 16 Jun 2020 09:13:59: 21000000 INFO @ Tue, 16 Jun 2020 09:14:03: 16000000 INFO @ Tue, 16 Jun 2020 09:14:07: 22000000 INFO @ Tue, 16 Jun 2020 09:14:12: 17000000 INFO @ Tue, 16 Jun 2020 09:14:16: #1 tag size is determined as 64 bps INFO @ Tue, 16 Jun 2020 09:14:16: #1 tag size = 64 INFO @ Tue, 16 Jun 2020 09:14:16: #1 total tags in treatment: 22998486 INFO @ Tue, 16 Jun 2020 09:14:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:14:16: #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 09:14:16: #1 tags after filtering in treatment: 22998486 INFO @ Tue, 16 Jun 2020 09:14:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:14:16: #1 finished! INFO @ Tue, 16 Jun 2020 09:14:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:14:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:14:18: #2 number of paired peaks: 158 WARNING @ Tue, 16 Jun 2020 09:14:18: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 16 Jun 2020 09:14:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:14:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:14:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:14:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:14:18: #2 predicted fragment length is 58 bps INFO @ Tue, 16 Jun 2020 09:14:18: #2 alternative fragment length(s) may be 2,58,577 bps INFO @ Tue, 16 Jun 2020 09:14:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.10_model.r WARNING @ Tue, 16 Jun 2020 09:14:18: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:14:18: #2 You may need to consider one of the other alternative d(s): 2,58,577 WARNING @ Tue, 16 Jun 2020 09:14:18: #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 09:14:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:14:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:14:21: 18000000 INFO @ Tue, 16 Jun 2020 09:14:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:29: 19000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:14:37: 20000000 INFO @ Tue, 16 Jun 2020 09:14:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.05_summits.bed INFO @ Tue, 16 Jun 2020 09:14:45: Done! INFO @ Tue, 16 Jun 2020 09:14:45: 21000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (993 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:14:53: 22000000 INFO @ Tue, 16 Jun 2020 09:14:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:15:01: #1 tag size is determined as 64 bps INFO @ Tue, 16 Jun 2020 09:15:01: #1 tag size = 64 INFO @ Tue, 16 Jun 2020 09:15:01: #1 total tags in treatment: 22998486 INFO @ Tue, 16 Jun 2020 09:15:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:15:01: #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 09:15:02: #1 tags after filtering in treatment: 22998486 INFO @ Tue, 16 Jun 2020 09:15:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:15:02: #1 finished! INFO @ Tue, 16 Jun 2020 09:15:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:15:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:15:03: #2 number of paired peaks: 158 WARNING @ Tue, 16 Jun 2020 09:15:03: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 16 Jun 2020 09:15:03: start model_add_line... INFO @ Tue, 16 Jun 2020 09:15:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:15:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:15:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:15:04: #2 predicted fragment length is 58 bps INFO @ Tue, 16 Jun 2020 09:15:04: #2 alternative fragment length(s) may be 2,58,577 bps INFO @ Tue, 16 Jun 2020 09:15:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.20_model.r WARNING @ Tue, 16 Jun 2020 09:15:04: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:15:04: #2 You may need to consider one of the other alternative d(s): 2,58,577 WARNING @ Tue, 16 Jun 2020 09:15:04: #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 09:15:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:15:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:15:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:15:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:15:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.10_summits.bed INFO @ Tue, 16 Jun 2020 09:15:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (614 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:15:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194211/SRX4194211.20_summits.bed INFO @ Tue, 16 Jun 2020 09:16:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (284 records, 4 fields): 2 millis CompletedMACS2peakCalling