Job ID = 6366765 SRX = SRX2228918 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:53:56 prefetch.2.10.7: 1) Downloading 'SRR4380374'... 2020-06-15T22:53:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:55:22 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:55:23 prefetch.2.10.7: 'SRR4380374' is valid 2020-06-15T22:55:23 prefetch.2.10.7: 1) 'SRR4380374' was downloaded successfully Read 20952107 spots for SRR4380374/SRR4380374.sra Written 20952107 spots for SRR4380374/SRR4380374.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: 00:03:21 20952107 reads; of these: 20952107 (100.00%) were unpaired; of these: 613887 (2.93%) aligned 0 times 16790339 (80.14%) aligned exactly 1 time 3547881 (16.93%) aligned >1 times 97.07% overall alignment rate Time searching: 00:03:21 Overall time: 00:03:21 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 8 files... [bam_rmdupse_core] 2048470 / 20338220 = 0.1007 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 08:03:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.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 08:03:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:10: 1000000 INFO @ Tue, 16 Jun 2020 08:03:14: 2000000 INFO @ Tue, 16 Jun 2020 08:03:19: 3000000 INFO @ Tue, 16 Jun 2020 08:03:23: 4000000 INFO @ Tue, 16 Jun 2020 08:03:28: 5000000 INFO @ Tue, 16 Jun 2020 08:03:32: 6000000 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 08:03:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.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 08:03:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:03:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:03:37: 7000000 INFO @ Tue, 16 Jun 2020 08:03:41: 1000000 INFO @ Tue, 16 Jun 2020 08:03:42: 8000000 INFO @ Tue, 16 Jun 2020 08:03:46: 2000000 INFO @ Tue, 16 Jun 2020 08:03:47: 9000000 INFO @ Tue, 16 Jun 2020 08:03:51: 3000000 INFO @ Tue, 16 Jun 2020 08:03:51: 10000000 INFO @ Tue, 16 Jun 2020 08:03:56: 4000000 INFO @ Tue, 16 Jun 2020 08:03:56: 11000000 INFO @ Tue, 16 Jun 2020 08:04:01: 5000000 INFO @ Tue, 16 Jun 2020 08:04:01: 12000000 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 08:04:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.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 08:04:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:06: 13000000 INFO @ Tue, 16 Jun 2020 08:04:07: 6000000 INFO @ Tue, 16 Jun 2020 08:04:11: 1000000 INFO @ Tue, 16 Jun 2020 08:04:11: 14000000 INFO @ Tue, 16 Jun 2020 08:04:12: 7000000 INFO @ Tue, 16 Jun 2020 08:04:16: 15000000 INFO @ Tue, 16 Jun 2020 08:04:17: 2000000 INFO @ Tue, 16 Jun 2020 08:04:18: 8000000 INFO @ Tue, 16 Jun 2020 08:04:21: 16000000 INFO @ Tue, 16 Jun 2020 08:04:22: 3000000 INFO @ Tue, 16 Jun 2020 08:04:23: 9000000 INFO @ Tue, 16 Jun 2020 08:04:26: 17000000 INFO @ Tue, 16 Jun 2020 08:04:28: 4000000 INFO @ Tue, 16 Jun 2020 08:04:29: 10000000 INFO @ Tue, 16 Jun 2020 08:04:31: 18000000 INFO @ Tue, 16 Jun 2020 08:04:33: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:04:33: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:04:33: #1 total tags in treatment: 18289750 INFO @ Tue, 16 Jun 2020 08:04:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:04:33: #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 08:04:33: 5000000 INFO @ Tue, 16 Jun 2020 08:04:33: #1 tags after filtering in treatment: 18289750 INFO @ Tue, 16 Jun 2020 08:04:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:04:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:04:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:04:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:04:34: #2 number of paired peaks: 236 WARNING @ Tue, 16 Jun 2020 08:04:34: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 16 Jun 2020 08:04:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:04:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:04:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:04:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:04:35: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:04:35: #2 alternative fragment length(s) may be 1,31,86,514,573 bps INFO @ Tue, 16 Jun 2020 08:04:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.05_model.r WARNING @ Tue, 16 Jun 2020 08:04:35: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:04:35: #2 You may need to consider one of the other alternative d(s): 1,31,86,514,573 WARNING @ Tue, 16 Jun 2020 08:04:35: #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 08:04:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:04:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:04:35: 11000000 INFO @ Tue, 16 Jun 2020 08:04:39: 6000000 INFO @ Tue, 16 Jun 2020 08:04:40: 12000000 INFO @ Tue, 16 Jun 2020 08:04:44: 7000000 INFO @ Tue, 16 Jun 2020 08:04:46: 13000000 INFO @ Tue, 16 Jun 2020 08:04:50: 8000000 INFO @ Tue, 16 Jun 2020 08:04:52: 14000000 INFO @ Tue, 16 Jun 2020 08:04:55: 9000000 INFO @ Tue, 16 Jun 2020 08:04:57: 15000000 INFO @ Tue, 16 Jun 2020 08:05:01: 10000000 INFO @ Tue, 16 Jun 2020 08:05:03: 16000000 INFO @ Tue, 16 Jun 2020 08:05:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:05:06: 11000000 INFO @ Tue, 16 Jun 2020 08:05:09: 17000000 INFO @ Tue, 16 Jun 2020 08:05:12: 12000000 INFO @ Tue, 16 Jun 2020 08:05:14: 18000000 INFO @ Tue, 16 Jun 2020 08:05:16: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:05:16: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:05:16: #1 total tags in treatment: 18289750 INFO @ Tue, 16 Jun 2020 08:05:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:16: #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 08:05:16: #1 tags after filtering in treatment: 18289750 INFO @ Tue, 16 Jun 2020 08:05:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:17: 13000000 INFO @ Tue, 16 Jun 2020 08:05:17: #2 number of paired peaks: 236 WARNING @ Tue, 16 Jun 2020 08:05:17: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 16 Jun 2020 08:05:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:17: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:05:17: #2 alternative fragment length(s) may be 1,31,86,514,573 bps INFO @ Tue, 16 Jun 2020 08:05:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.10_model.r WARNING @ Tue, 16 Jun 2020 08:05:17: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:05:17: #2 You may need to consider one of the other alternative d(s): 1,31,86,514,573 WARNING @ Tue, 16 Jun 2020 08:05:17: #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 08:05:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:05:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:05:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:05:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.05_summits.bed INFO @ Tue, 16 Jun 2020 08:05:18: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (655 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:05:22: 14000000 INFO @ Tue, 16 Jun 2020 08:05:27: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:05:33: 16000000 INFO @ Tue, 16 Jun 2020 08:05:38: 17000000 INFO @ Tue, 16 Jun 2020 08:05:43: 18000000 INFO @ Tue, 16 Jun 2020 08:05:44: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:05:44: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:05:44: #1 total tags in treatment: 18289750 INFO @ Tue, 16 Jun 2020 08:05:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:05:44: #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 08:05:45: #1 tags after filtering in treatment: 18289750 INFO @ Tue, 16 Jun 2020 08:05:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:05:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:05:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:05:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:05:46: #2 number of paired peaks: 236 WARNING @ Tue, 16 Jun 2020 08:05:46: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 16 Jun 2020 08:05:46: start model_add_line... INFO @ Tue, 16 Jun 2020 08:05:46: start X-correlation... INFO @ Tue, 16 Jun 2020 08:05:46: end of X-cor INFO @ Tue, 16 Jun 2020 08:05:46: #2 finished! INFO @ Tue, 16 Jun 2020 08:05:46: #2 predicted fragment length is 31 bps INFO @ Tue, 16 Jun 2020 08:05:46: #2 alternative fragment length(s) may be 1,31,86,514,573 bps INFO @ Tue, 16 Jun 2020 08:05:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.20_model.r WARNING @ Tue, 16 Jun 2020 08:05:46: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:05:46: #2 You may need to consider one of the other alternative d(s): 1,31,86,514,573 WARNING @ Tue, 16 Jun 2020 08:05:46: #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 08:05:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:05:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:05:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.10_summits.bed INFO @ Tue, 16 Jun 2020 08:06:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (280 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:06:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:06:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:06:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:06:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228918/SRX2228918.20_summits.bed INFO @ Tue, 16 Jun 2020 08:06:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (62 records, 4 fields): 1 millis CompletedMACS2peakCalling