Job ID = 6368646 SRX = SRX529206 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:27:16 prefetch.2.10.7: 1) Downloading 'SRR1265810'... 2020-06-16T00:27:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:28:13 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:28:13 prefetch.2.10.7: 'SRR1265810' is valid 2020-06-16T00:28:13 prefetch.2.10.7: 1) 'SRR1265810' was downloaded successfully Read 9807251 spots for SRR1265810/SRR1265810.sra Written 9807251 spots for SRR1265810/SRR1265810.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: 00:01:44 9807251 reads; of these: 9807251 (100.00%) were unpaired; of these: 293439 (2.99%) aligned 0 times 7730063 (78.82%) aligned exactly 1 time 1783749 (18.19%) aligned >1 times 97.01% overall alignment rate Time searching: 00:01:44 Overall time: 00:01:44 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_rmdupse_core] 784431 / 9513812 = 0.0825 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 09:33:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.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 09:33:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:22: 1000000 INFO @ Tue, 16 Jun 2020 09:33:26: 2000000 INFO @ Tue, 16 Jun 2020 09:33:31: 3000000 INFO @ Tue, 16 Jun 2020 09:33:35: 4000000 INFO @ Tue, 16 Jun 2020 09:33:40: 5000000 INFO @ Tue, 16 Jun 2020 09:33:44: 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 09:33:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.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 09:33:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:49: 7000000 INFO @ Tue, 16 Jun 2020 09:33:52: 1000000 INFO @ Tue, 16 Jun 2020 09:33:54: 8000000 INFO @ Tue, 16 Jun 2020 09:33:57: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:33:57: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:33:57: #1 total tags in treatment: 8729381 INFO @ Tue, 16 Jun 2020 09:33:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:57: #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 09:33:58: #1 tags after filtering in treatment: 8729381 INFO @ Tue, 16 Jun 2020 09:33:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:58: 2000000 INFO @ Tue, 16 Jun 2020 09:33:58: #2 number of paired peaks: 314 WARNING @ Tue, 16 Jun 2020 09:33:58: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:58: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:58: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:58: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:58: #2 predicted fragment length is 36 bps INFO @ Tue, 16 Jun 2020 09:33:58: #2 alternative fragment length(s) may be 3,36 bps INFO @ Tue, 16 Jun 2020 09:33:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.05_model.r WARNING @ Tue, 16 Jun 2020 09:33:58: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:33:58: #2 You may need to consider one of the other alternative d(s): 3,36 WARNING @ Tue, 16 Jun 2020 09:33:58: #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 09:33:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:03: 3000000 INFO @ Tue, 16 Jun 2020 09:34:08: 4000000 INFO @ Tue, 16 Jun 2020 09:34:14: 5000000 INFO @ Tue, 16 Jun 2020 09:34:15: #3 Call peaks for each chromosome... 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 09:34:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.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 09:34:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:19: 6000000 INFO @ Tue, 16 Jun 2020 09:34:22: 1000000 INFO @ Tue, 16 Jun 2020 09:34:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.05_summits.bed INFO @ Tue, 16 Jun 2020 09:34:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1224 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:34:24: 7000000 INFO @ Tue, 16 Jun 2020 09:34:28: 2000000 INFO @ Tue, 16 Jun 2020 09:34:30: 8000000 INFO @ Tue, 16 Jun 2020 09:34:33: 3000000 INFO @ Tue, 16 Jun 2020 09:34:34: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:34:34: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:34:34: #1 total tags in treatment: 8729381 INFO @ Tue, 16 Jun 2020 09:34:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:34: #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 09:34:34: #1 tags after filtering in treatment: 8729381 INFO @ Tue, 16 Jun 2020 09:34:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:34:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:34: #2 number of paired peaks: 314 WARNING @ Tue, 16 Jun 2020 09:34:34: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:34: #2 predicted fragment length is 36 bps INFO @ Tue, 16 Jun 2020 09:34:34: #2 alternative fragment length(s) may be 3,36 bps INFO @ Tue, 16 Jun 2020 09:34:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.10_model.r WARNING @ Tue, 16 Jun 2020 09:34:34: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:34:34: #2 You may need to consider one of the other alternative d(s): 3,36 WARNING @ Tue, 16 Jun 2020 09:34:34: #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 09:34:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:38: 4000000 INFO @ Tue, 16 Jun 2020 09:34:44: 5000000 INFO @ Tue, 16 Jun 2020 09:34:49: 6000000 INFO @ Tue, 16 Jun 2020 09:34:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:34:54: 7000000 INFO @ Tue, 16 Jun 2020 09:34:59: 8000000 INFO @ Tue, 16 Jun 2020 09:35:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.10_summits.bed INFO @ Tue, 16 Jun 2020 09:35:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (328 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:35:03: #1 tag size is determined as 36 bps INFO @ Tue, 16 Jun 2020 09:35:03: #1 tag size = 36 INFO @ Tue, 16 Jun 2020 09:35:03: #1 total tags in treatment: 8729381 INFO @ Tue, 16 Jun 2020 09:35:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:03: #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 09:35:04: #1 tags after filtering in treatment: 8729381 INFO @ Tue, 16 Jun 2020 09:35:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:04: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:04: #2 number of paired peaks: 314 WARNING @ Tue, 16 Jun 2020 09:35:04: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:04: #2 predicted fragment length is 36 bps INFO @ Tue, 16 Jun 2020 09:35:04: #2 alternative fragment length(s) may be 3,36 bps INFO @ Tue, 16 Jun 2020 09:35:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.20_model.r WARNING @ Tue, 16 Jun 2020 09:35:04: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:04: #2 You may need to consider one of the other alternative d(s): 3,36 WARNING @ Tue, 16 Jun 2020 09:35:04: #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 09:35:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:35:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX529206/SRX529206.20_summits.bed INFO @ Tue, 16 Jun 2020 09:35:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (97 records, 4 fields): 1 millis CompletedMACS2peakCalling