Job ID = 6367585 SRX = SRX331342 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:27:36 prefetch.2.10.7: 1) Downloading 'SRR947579'... 2020-06-15T23:27:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:30:09 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:30:10 prefetch.2.10.7: 'SRR947579' is valid 2020-06-15T23:30:10 prefetch.2.10.7: 1) 'SRR947579' was downloaded successfully Read 19040559 spots for SRR947579/SRR947579.sra Written 19040559 spots for SRR947579/SRR947579.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: 00:04:11 19040559 reads; of these: 19040559 (100.00%) were unpaired; of these: 793487 (4.17%) aligned 0 times 15280731 (80.25%) aligned exactly 1 time 2966341 (15.58%) aligned >1 times 95.83% overall alignment rate Time searching: 00:04:11 Overall time: 00:04:11 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] 10944049 / 18247072 = 0.5998 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 08:38:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.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 08:38:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:38:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:38:24: 1000000 INFO @ Tue, 16 Jun 2020 08:38:28: 2000000 INFO @ Tue, 16 Jun 2020 08:38:32: 3000000 INFO @ Tue, 16 Jun 2020 08:38:37: 4000000 INFO @ Tue, 16 Jun 2020 08:38:41: 5000000 INFO @ Tue, 16 Jun 2020 08:38:46: 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 08:38:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.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 08:38:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:38:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:38:50: 7000000 INFO @ Tue, 16 Jun 2020 08:38:52: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:38:52: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:38:52: #1 total tags in treatment: 7303023 INFO @ Tue, 16 Jun 2020 08:38:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:38:52: #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 08:38:52: #1 tags after filtering in treatment: 7303023 INFO @ Tue, 16 Jun 2020 08:38:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:38:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:38:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:38:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:38:52: #2 number of paired peaks: 517 WARNING @ Tue, 16 Jun 2020 08:38:52: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Tue, 16 Jun 2020 08:38:52: start model_add_line... INFO @ Tue, 16 Jun 2020 08:38:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:38:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:38:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:38:53: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:38:53: #2 alternative fragment length(s) may be 3,47,527 bps INFO @ Tue, 16 Jun 2020 08:38:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.05_model.r WARNING @ Tue, 16 Jun 2020 08:38:53: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:38:53: #2 You may need to consider one of the other alternative d(s): 3,47,527 WARNING @ Tue, 16 Jun 2020 08:38:53: #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 08:38:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:38:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:38:54: 1000000 INFO @ Tue, 16 Jun 2020 08:38:58: 2000000 INFO @ Tue, 16 Jun 2020 08:39:03: 3000000 INFO @ Tue, 16 Jun 2020 08:39:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:39:07: 4000000 INFO @ Tue, 16 Jun 2020 08:39:12: 5000000 INFO @ Tue, 16 Jun 2020 08:39:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:39:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:39:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.05_summits.bed INFO @ Tue, 16 Jun 2020 08:39:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (796 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:39:16: 6000000 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 08:39:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.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 08:39:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:21: 7000000 INFO @ Tue, 16 Jun 2020 08:39:22: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:39:22: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:39:22: #1 total tags in treatment: 7303023 INFO @ Tue, 16 Jun 2020 08:39:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:39:22: #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 08:39:22: #1 tags after filtering in treatment: 7303023 INFO @ Tue, 16 Jun 2020 08:39:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:39:22: #1 finished! INFO @ Tue, 16 Jun 2020 08:39:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:39:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:39:23: #2 number of paired peaks: 517 WARNING @ Tue, 16 Jun 2020 08:39:23: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Tue, 16 Jun 2020 08:39:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:39:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:39:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:39:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:39:23: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:39:23: #2 alternative fragment length(s) may be 3,47,527 bps INFO @ Tue, 16 Jun 2020 08:39:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.10_model.r WARNING @ Tue, 16 Jun 2020 08:39:23: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:39:23: #2 You may need to consider one of the other alternative d(s): 3,47,527 WARNING @ Tue, 16 Jun 2020 08:39:23: #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 08:39:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:39:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:39:24: 1000000 INFO @ Tue, 16 Jun 2020 08:39:28: 2000000 INFO @ Tue, 16 Jun 2020 08:39:33: 3000000 INFO @ Tue, 16 Jun 2020 08:39:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:39:38: 4000000 INFO @ Tue, 16 Jun 2020 08:39:42: 5000000 INFO @ Tue, 16 Jun 2020 08:39:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:39:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:39:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.10_summits.bed INFO @ Tue, 16 Jun 2020 08:39:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (558 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:39:47: 6000000 INFO @ Tue, 16 Jun 2020 08:39:51: 7000000 INFO @ Tue, 16 Jun 2020 08:39:53: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:39:53: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:39:53: #1 total tags in treatment: 7303023 INFO @ Tue, 16 Jun 2020 08:39:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:39:53: #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 08:39:53: #1 tags after filtering in treatment: 7303023 INFO @ Tue, 16 Jun 2020 08:39:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:39:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:39:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:39:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:39:53: #2 number of paired peaks: 517 WARNING @ Tue, 16 Jun 2020 08:39:53: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Tue, 16 Jun 2020 08:39:53: start model_add_line... INFO @ Tue, 16 Jun 2020 08:39:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:39:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:39:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:39:53: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:39:53: #2 alternative fragment length(s) may be 3,47,527 bps INFO @ Tue, 16 Jun 2020 08:39:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.20_model.r WARNING @ Tue, 16 Jun 2020 08:39:53: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:39:53: #2 You may need to consider one of the other alternative d(s): 3,47,527 WARNING @ Tue, 16 Jun 2020 08:39:53: #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 08:39:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:39:53: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:40:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:40:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331342/SRX331342.20_summits.bed INFO @ Tue, 16 Jun 2020 08:40:15: Done! BigWig に変換しました。 pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (232 records, 4 fields): 1 millis CompletedMACS2peakCalling