Job ID = 6368366 SRX = SRX495046 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:04:15 prefetch.2.10.7: 1) Downloading 'SRR1198578'... 2020-06-16T00:04:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:08:50 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:08:50 prefetch.2.10.7: 1) 'SRR1198578' was downloaded successfully Read 22634552 spots for SRR1198578/SRR1198578.sra Written 22634552 spots for SRR1198578/SRR1198578.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: 00:03:41 22634552 reads; of these: 22634552 (100.00%) were unpaired; of these: 3508049 (15.50%) aligned 0 times 16088556 (71.08%) aligned exactly 1 time 3037947 (13.42%) aligned >1 times 84.50% overall alignment rate Time searching: 00:03:41 Overall time: 00:03:41 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] 3757855 / 19126503 = 0.1965 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 09:18:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.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 09:18:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:18: 1000000 INFO @ Tue, 16 Jun 2020 09:18:23: 2000000 INFO @ Tue, 16 Jun 2020 09:18:28: 3000000 INFO @ Tue, 16 Jun 2020 09:18:33: 4000000 INFO @ Tue, 16 Jun 2020 09:18:39: 5000000 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 09:18:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.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 09:18:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:44: 6000000 INFO @ Tue, 16 Jun 2020 09:18:49: 1000000 INFO @ Tue, 16 Jun 2020 09:18:50: 7000000 INFO @ Tue, 16 Jun 2020 09:18:56: 8000000 INFO @ Tue, 16 Jun 2020 09:18:56: 2000000 INFO @ Tue, 16 Jun 2020 09:19:02: 9000000 INFO @ Tue, 16 Jun 2020 09:19:03: 3000000 INFO @ Tue, 16 Jun 2020 09:19:08: 10000000 INFO @ Tue, 16 Jun 2020 09:19:10: 4000000 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 09:19:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.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 09:19:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:14: 11000000 INFO @ Tue, 16 Jun 2020 09:19:17: 5000000 INFO @ Tue, 16 Jun 2020 09:19:18: 1000000 INFO @ Tue, 16 Jun 2020 09:19:20: 12000000 INFO @ Tue, 16 Jun 2020 09:19:23: 6000000 INFO @ Tue, 16 Jun 2020 09:19:24: 2000000 INFO @ Tue, 16 Jun 2020 09:19:26: 13000000 INFO @ Tue, 16 Jun 2020 09:19:29: 7000000 INFO @ Tue, 16 Jun 2020 09:19:30: 3000000 INFO @ Tue, 16 Jun 2020 09:19:32: 14000000 INFO @ Tue, 16 Jun 2020 09:19:36: 8000000 INFO @ Tue, 16 Jun 2020 09:19:36: 4000000 INFO @ Tue, 16 Jun 2020 09:19:37: 15000000 INFO @ Tue, 16 Jun 2020 09:19:40: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:19:40: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:19:40: #1 total tags in treatment: 15368648 INFO @ Tue, 16 Jun 2020 09:19:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:19:40: #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 09:19:40: #1 tags after filtering in treatment: 15368648 INFO @ Tue, 16 Jun 2020 09:19:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:19:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:19:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:19:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:19:41: #2 number of paired peaks: 267 WARNING @ Tue, 16 Jun 2020 09:19:41: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Tue, 16 Jun 2020 09:19:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:19:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:19:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:19:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:19:41: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:19:41: #2 alternative fragment length(s) may be 2,45,561,566 bps INFO @ Tue, 16 Jun 2020 09:19:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.05_model.r WARNING @ Tue, 16 Jun 2020 09:19:41: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:19:41: #2 You may need to consider one of the other alternative d(s): 2,45,561,566 WARNING @ Tue, 16 Jun 2020 09:19:41: #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 09:19:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:19:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:19:42: 5000000 INFO @ Tue, 16 Jun 2020 09:19:42: 9000000 INFO @ Tue, 16 Jun 2020 09:19:48: 6000000 INFO @ Tue, 16 Jun 2020 09:19:49: 10000000 INFO @ Tue, 16 Jun 2020 09:19:54: 7000000 INFO @ Tue, 16 Jun 2020 09:19:55: 11000000 INFO @ Tue, 16 Jun 2020 09:20:00: 8000000 INFO @ Tue, 16 Jun 2020 09:20:02: 12000000 INFO @ Tue, 16 Jun 2020 09:20:06: 9000000 INFO @ Tue, 16 Jun 2020 09:20:08: 13000000 INFO @ Tue, 16 Jun 2020 09:20:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:11: 10000000 INFO @ Tue, 16 Jun 2020 09:20:15: 14000000 INFO @ Tue, 16 Jun 2020 09:20:17: 11000000 INFO @ Tue, 16 Jun 2020 09:20:22: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:20:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.05_summits.bed INFO @ Tue, 16 Jun 2020 09:20:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (700 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:20:23: 12000000 INFO @ Tue, 16 Jun 2020 09:20:24: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:20:24: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:20:24: #1 total tags in treatment: 15368648 INFO @ Tue, 16 Jun 2020 09:20:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:24: #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 09:20:24: #1 tags after filtering in treatment: 15368648 INFO @ Tue, 16 Jun 2020 09:20:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:25: #2 number of paired peaks: 267 WARNING @ Tue, 16 Jun 2020 09:20:25: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:26: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:20:26: #2 alternative fragment length(s) may be 2,45,561,566 bps INFO @ Tue, 16 Jun 2020 09:20:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.10_model.r WARNING @ Tue, 16 Jun 2020 09:20:26: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:26: #2 You may need to consider one of the other alternative d(s): 2,45,561,566 WARNING @ Tue, 16 Jun 2020 09:20:26: #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 09:20:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:29: 13000000 INFO @ Tue, 16 Jun 2020 09:20:34: 14000000 INFO @ Tue, 16 Jun 2020 09:20:40: 15000000 INFO @ Tue, 16 Jun 2020 09:20:42: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:20:42: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:20:42: #1 total tags in treatment: 15368648 INFO @ Tue, 16 Jun 2020 09:20:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:42: #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 09:20:42: #1 tags after filtering in treatment: 15368648 INFO @ Tue, 16 Jun 2020 09:20:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:20:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:43: #2 number of paired peaks: 267 WARNING @ Tue, 16 Jun 2020 09:20:43: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:43: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:20:43: #2 alternative fragment length(s) may be 2,45,561,566 bps INFO @ Tue, 16 Jun 2020 09:20:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.20_model.r WARNING @ Tue, 16 Jun 2020 09:20:43: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:43: #2 You may need to consider one of the other alternative d(s): 2,45,561,566 WARNING @ Tue, 16 Jun 2020 09:20:43: #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 09:20:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:52: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:21:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.10_summits.bed INFO @ Tue, 16 Jun 2020 09:21:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (351 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:21:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495046/SRX495046.20_summits.bed INFO @ Tue, 16 Jun 2020 09:21:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (128 records, 4 fields): 1 millis CompletedMACS2peakCalling