Job ID = 6507882 SRX = SRX494967 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T12:50:32 prefetch.2.10.7: 1) Downloading 'SRR1198499'... 2020-06-26T12:50:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T12:51:57 prefetch.2.10.7: HTTPS download succeed 2020-06-26T12:51:58 prefetch.2.10.7: 'SRR1198499' is valid 2020-06-26T12:51:58 prefetch.2.10.7: 1) 'SRR1198499' was downloaded successfully Read 14315583 spots for SRR1198499/SRR1198499.sra Written 14315583 spots for SRR1198499/SRR1198499.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: 00:03:12 14315583 reads; of these: 14315583 (100.00%) were unpaired; of these: 295081 (2.06%) aligned 0 times 11731729 (81.95%) aligned exactly 1 time 2288773 (15.99%) aligned >1 times 97.94% overall alignment rate Time searching: 00:03:12 Overall time: 00:03:12 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] 4768770 / 14020502 = 0.3401 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 @ Fri, 26 Jun 2020 21:58:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.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 @ Fri, 26 Jun 2020 21:58:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 21:58:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 21:58:53: 1000000 INFO @ Fri, 26 Jun 2020 21:58:58: 2000000 INFO @ Fri, 26 Jun 2020 21:59:03: 3000000 INFO @ Fri, 26 Jun 2020 21:59:08: 4000000 INFO @ Fri, 26 Jun 2020 21:59:13: 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 @ Fri, 26 Jun 2020 21:59:18: 6000000 INFO @ Fri, 26 Jun 2020 21:59:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.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 @ Fri, 26 Jun 2020 21:59:19: #1 read tag files... INFO @ Fri, 26 Jun 2020 21:59:19: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 21:59:23: 7000000 INFO @ Fri, 26 Jun 2020 21:59:24: 1000000 INFO @ Fri, 26 Jun 2020 21:59:28: 8000000 INFO @ Fri, 26 Jun 2020 21:59:29: 2000000 INFO @ Fri, 26 Jun 2020 21:59:33: 9000000 INFO @ Fri, 26 Jun 2020 21:59:34: 3000000 INFO @ Fri, 26 Jun 2020 21:59:34: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 21:59:34: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 21:59:34: #1 total tags in treatment: 9251732 INFO @ Fri, 26 Jun 2020 21:59:34: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 21:59:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 21:59:34: #1 tags after filtering in treatment: 9251732 INFO @ Fri, 26 Jun 2020 21:59:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 21:59:34: #1 finished! INFO @ Fri, 26 Jun 2020 21:59:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 21:59:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 21:59:35: #2 number of paired peaks: 388 WARNING @ Fri, 26 Jun 2020 21:59:35: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Fri, 26 Jun 2020 21:59:35: start model_add_line... INFO @ Fri, 26 Jun 2020 21:59:35: start X-correlation... INFO @ Fri, 26 Jun 2020 21:59:35: end of X-cor INFO @ Fri, 26 Jun 2020 21:59:35: #2 finished! INFO @ Fri, 26 Jun 2020 21:59:35: #2 predicted fragment length is 50 bps INFO @ Fri, 26 Jun 2020 21:59:35: #2 alternative fragment length(s) may be 2,50 bps INFO @ Fri, 26 Jun 2020 21:59:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.05_model.r WARNING @ Fri, 26 Jun 2020 21:59:35: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 21:59:35: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Fri, 26 Jun 2020 21:59:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 21:59:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 21:59:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 21:59:39: 4000000 INFO @ Fri, 26 Jun 2020 21:59:44: 5000000 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 @ Fri, 26 Jun 2020 21:59:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.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 @ Fri, 26 Jun 2020 21:59:49: #1 read tag files... INFO @ Fri, 26 Jun 2020 21:59:49: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 21:59:49: 6000000 INFO @ Fri, 26 Jun 2020 21:59:54: 1000000 INFO @ Fri, 26 Jun 2020 21:59:54: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 21:59:55: 7000000 INFO @ Fri, 26 Jun 2020 21:59:59: 2000000 INFO @ Fri, 26 Jun 2020 22:00:00: 8000000 INFO @ Fri, 26 Jun 2020 22:00:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:00:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:00:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.05_summits.bed INFO @ Fri, 26 Jun 2020 22:00:04: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (712 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:00:04: 3000000 INFO @ Fri, 26 Jun 2020 22:00:05: 9000000 INFO @ Fri, 26 Jun 2020 22:00:07: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:00:07: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:00:07: #1 total tags in treatment: 9251732 INFO @ Fri, 26 Jun 2020 22:00:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:00:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:00:07: #1 tags after filtering in treatment: 9251732 INFO @ Fri, 26 Jun 2020 22:00:07: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:00:07: #1 finished! INFO @ Fri, 26 Jun 2020 22:00:07: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:00:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:00:07: #2 number of paired peaks: 388 WARNING @ Fri, 26 Jun 2020 22:00:07: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Fri, 26 Jun 2020 22:00:07: start model_add_line... INFO @ Fri, 26 Jun 2020 22:00:07: start X-correlation... INFO @ Fri, 26 Jun 2020 22:00:07: end of X-cor INFO @ Fri, 26 Jun 2020 22:00:07: #2 finished! INFO @ Fri, 26 Jun 2020 22:00:07: #2 predicted fragment length is 50 bps INFO @ Fri, 26 Jun 2020 22:00:07: #2 alternative fragment length(s) may be 2,50 bps INFO @ Fri, 26 Jun 2020 22:00:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.10_model.r WARNING @ Fri, 26 Jun 2020 22:00:07: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:00:07: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Fri, 26 Jun 2020 22:00:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:00:07: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:00:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:00:10: 4000000 INFO @ Fri, 26 Jun 2020 22:00:15: 5000000 INFO @ Fri, 26 Jun 2020 22:00:20: 6000000 INFO @ Fri, 26 Jun 2020 22:00:25: 7000000 INFO @ Fri, 26 Jun 2020 22:00:27: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:00:30: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:00:35: 9000000 INFO @ Fri, 26 Jun 2020 22:00:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:00:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:00:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.10_summits.bed INFO @ Fri, 26 Jun 2020 22:00:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (464 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:00:36: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:00:36: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:00:36: #1 total tags in treatment: 9251732 INFO @ Fri, 26 Jun 2020 22:00:36: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:00:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:00:36: #1 tags after filtering in treatment: 9251732 INFO @ Fri, 26 Jun 2020 22:00:36: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:00:36: #1 finished! INFO @ Fri, 26 Jun 2020 22:00:36: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:00:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:00:37: #2 number of paired peaks: 388 WARNING @ Fri, 26 Jun 2020 22:00:37: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Fri, 26 Jun 2020 22:00:37: start model_add_line... INFO @ Fri, 26 Jun 2020 22:00:37: start X-correlation... INFO @ Fri, 26 Jun 2020 22:00:37: end of X-cor INFO @ Fri, 26 Jun 2020 22:00:37: #2 finished! INFO @ Fri, 26 Jun 2020 22:00:37: #2 predicted fragment length is 50 bps INFO @ Fri, 26 Jun 2020 22:00:37: #2 alternative fragment length(s) may be 2,50 bps INFO @ Fri, 26 Jun 2020 22:00:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.20_model.r WARNING @ Fri, 26 Jun 2020 22:00:37: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:00:37: #2 You may need to consider one of the other alternative d(s): 2,50 WARNING @ Fri, 26 Jun 2020 22:00:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:00:37: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:00:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:00:56: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:01:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:01:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:01:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494967/SRX494967.20_summits.bed INFO @ Fri, 26 Jun 2020 22:01:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (192 records, 4 fields): 1 millis CompletedMACS2peakCalling