Job ID = 6366557 SRX = SRX1936235 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:55:29 prefetch.2.10.7: 1) Downloading 'SRR3879841'... 2020-06-15T22:55:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:56:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:56:53 prefetch.2.10.7: 'SRR3879841' is valid 2020-06-15T22:56:53 prefetch.2.10.7: 1) 'SRR3879841' was downloaded successfully Read 18019537 spots for SRR3879841/SRR3879841.sra Written 18019537 spots for SRR3879841/SRR3879841.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: 00:04:21 18019537 reads; of these: 18019537 (100.00%) were unpaired; of these: 572251 (3.18%) aligned 0 times 14980323 (83.13%) aligned exactly 1 time 2466963 (13.69%) aligned >1 times 96.82% overall alignment rate Time searching: 00:04:21 Overall time: 00:04:21 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] 2065561 / 17447286 = 0.1184 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 08:06:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.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 08:06:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:06:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:06:43: 1000000 INFO @ Tue, 16 Jun 2020 08:06:49: 2000000 INFO @ Tue, 16 Jun 2020 08:06:55: 3000000 INFO @ Tue, 16 Jun 2020 08:07:01: 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 08:07:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.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 08:07:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:07: 5000000 INFO @ Tue, 16 Jun 2020 08:07:14: 1000000 INFO @ Tue, 16 Jun 2020 08:07:14: 6000000 INFO @ Tue, 16 Jun 2020 08:07:21: 2000000 INFO @ Tue, 16 Jun 2020 08:07:21: 7000000 INFO @ Tue, 16 Jun 2020 08:07:28: 8000000 INFO @ Tue, 16 Jun 2020 08:07:28: 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 08:07:35: 9000000 INFO @ Tue, 16 Jun 2020 08:07:35: 4000000 INFO @ Tue, 16 Jun 2020 08:07:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.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 08:07:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:42: 10000000 INFO @ Tue, 16 Jun 2020 08:07:43: 5000000 INFO @ Tue, 16 Jun 2020 08:07:45: 1000000 INFO @ Tue, 16 Jun 2020 08:07:50: 11000000 INFO @ Tue, 16 Jun 2020 08:07:52: 6000000 INFO @ Tue, 16 Jun 2020 08:07:53: 2000000 INFO @ Tue, 16 Jun 2020 08:07:58: 12000000 INFO @ Tue, 16 Jun 2020 08:08:00: 7000000 INFO @ Tue, 16 Jun 2020 08:08:02: 3000000 INFO @ Tue, 16 Jun 2020 08:08:06: 13000000 INFO @ Tue, 16 Jun 2020 08:08:07: 8000000 INFO @ Tue, 16 Jun 2020 08:08:11: 4000000 INFO @ Tue, 16 Jun 2020 08:08:14: 14000000 INFO @ Tue, 16 Jun 2020 08:08:15: 9000000 INFO @ Tue, 16 Jun 2020 08:08:20: 5000000 INFO @ Tue, 16 Jun 2020 08:08:21: 15000000 INFO @ Tue, 16 Jun 2020 08:08:23: 10000000 INFO @ Tue, 16 Jun 2020 08:08:24: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:08:24: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:08:24: #1 total tags in treatment: 15381725 INFO @ Tue, 16 Jun 2020 08:08:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:24: #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 08:08:24: #1 tags after filtering in treatment: 15381725 INFO @ Tue, 16 Jun 2020 08:08:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:25: #2 number of paired peaks: 120 WARNING @ Tue, 16 Jun 2020 08:08:25: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:26: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:08:26: #2 alternative fragment length(s) may be 2,52,121,503,530,561,580 bps INFO @ Tue, 16 Jun 2020 08:08:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.05_model.r WARNING @ Tue, 16 Jun 2020 08:08:26: #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 08:08:26: #2 You may need to consider one of the other alternative d(s): 2,52,121,503,530,561,580 WARNING @ Tue, 16 Jun 2020 08:08:26: #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 08:08:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:08:28: 6000000 INFO @ Tue, 16 Jun 2020 08:08:31: 11000000 INFO @ Tue, 16 Jun 2020 08:08:36: 7000000 INFO @ Tue, 16 Jun 2020 08:08:38: 12000000 INFO @ Tue, 16 Jun 2020 08:08:45: 8000000 INFO @ Tue, 16 Jun 2020 08:08:46: 13000000 INFO @ Tue, 16 Jun 2020 08:08:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:53: 9000000 INFO @ Tue, 16 Jun 2020 08:08:54: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:09:01: 15000000 INFO @ Tue, 16 Jun 2020 08:09:02: 10000000 INFO @ Tue, 16 Jun 2020 08:09:04: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:09:04: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:09:04: #1 total tags in treatment: 15381725 INFO @ Tue, 16 Jun 2020 08:09:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:04: #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 08:09:04: #1 tags after filtering in treatment: 15381725 INFO @ Tue, 16 Jun 2020 08:09:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:09:04: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:09:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.05_summits.bed INFO @ Tue, 16 Jun 2020 08:09:05: Done! INFO @ Tue, 16 Jun 2020 08:09:05: #2 number of paired peaks: 120 WARNING @ Tue, 16 Jun 2020 08:09:05: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Tue, 16 Jun 2020 08:09:05: start model_add_line... pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (550 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:09:06: start X-correlation... INFO @ Tue, 16 Jun 2020 08:09:06: end of X-cor INFO @ Tue, 16 Jun 2020 08:09:06: #2 finished! INFO @ Tue, 16 Jun 2020 08:09:06: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:09:06: #2 alternative fragment length(s) may be 2,52,121,503,530,561,580 bps INFO @ Tue, 16 Jun 2020 08:09:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.10_model.r WARNING @ Tue, 16 Jun 2020 08:09:06: #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 08:09:06: #2 You may need to consider one of the other alternative d(s): 2,52,121,503,530,561,580 WARNING @ Tue, 16 Jun 2020 08:09:06: #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 08:09:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:09:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:09:09: 11000000 INFO @ Tue, 16 Jun 2020 08:09:17: 12000000 INFO @ Tue, 16 Jun 2020 08:09:25: 13000000 INFO @ Tue, 16 Jun 2020 08:09:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:32: 14000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:09:40: 15000000 INFO @ Tue, 16 Jun 2020 08:09:43: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:09:43: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:09:43: #1 total tags in treatment: 15381725 INFO @ Tue, 16 Jun 2020 08:09:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:09:43: #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 08:09:43: #1 tags after filtering in treatment: 15381725 INFO @ Tue, 16 Jun 2020 08:09:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:09:43: #1 finished! INFO @ Tue, 16 Jun 2020 08:09:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:09:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:09:44: #2 number of paired peaks: 120 WARNING @ Tue, 16 Jun 2020 08:09:44: Fewer paired peaks (120) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 120 pairs to build model! INFO @ Tue, 16 Jun 2020 08:09:44: start model_add_line... INFO @ Tue, 16 Jun 2020 08:09:44: start X-correlation... INFO @ Tue, 16 Jun 2020 08:09:44: end of X-cor INFO @ Tue, 16 Jun 2020 08:09:44: #2 finished! INFO @ Tue, 16 Jun 2020 08:09:44: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:09:44: #2 alternative fragment length(s) may be 2,52,121,503,530,561,580 bps INFO @ Tue, 16 Jun 2020 08:09:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.20_model.r WARNING @ Tue, 16 Jun 2020 08:09:44: #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 08:09:44: #2 You may need to consider one of the other alternative d(s): 2,52,121,503,530,561,580 WARNING @ Tue, 16 Jun 2020 08:09:44: #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 08:09:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:09:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:09:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.10_summits.bed INFO @ Tue, 16 Jun 2020 08:09:46: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (311 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:10:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:10:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:10:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:10:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936235/SRX1936235.20_summits.bed INFO @ Tue, 16 Jun 2020 08:10:26: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (121 records, 4 fields): 1 millis CompletedMACS2peakCalling