Job ID = 6368009 SRX = SRX466472 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:55:03 prefetch.2.10.7: 1) Downloading 'SRR1163538'... 2020-06-15T23:55:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:55:49 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:55:49 prefetch.2.10.7: 'SRR1163538' is valid 2020-06-15T23:55:49 prefetch.2.10.7: 1) 'SRR1163538' was downloaded successfully Read 5595479 spots for SRR1163538/SRR1163538.sra Written 5595479 spots for SRR1163538/SRR1163538.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: 00:01:13 5595479 reads; of these: 5595479 (100.00%) were unpaired; of these: 127543 (2.28%) aligned 0 times 4499839 (80.42%) aligned exactly 1 time 968097 (17.30%) aligned >1 times 97.72% overall alignment rate Time searching: 00:01:13 Overall time: 00:01:13 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] 319571 / 5467936 = 0.0584 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 08:59:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.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 08:59:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:59:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:37: 1000000 INFO @ Tue, 16 Jun 2020 08:59:42: 2000000 INFO @ Tue, 16 Jun 2020 08:59:47: 3000000 INFO @ Tue, 16 Jun 2020 08:59:52: 4000000 INFO @ Tue, 16 Jun 2020 08:59:57: 5000000 INFO @ Tue, 16 Jun 2020 08:59:58: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:59:58: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:59:58: #1 total tags in treatment: 5148365 INFO @ Tue, 16 Jun 2020 08:59:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:59:58: #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 08:59:58: #1 tags after filtering in treatment: 5148365 INFO @ Tue, 16 Jun 2020 08:59:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:59:58: #1 finished! INFO @ Tue, 16 Jun 2020 08:59:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:59:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:59:58: #2 number of paired peaks: 446 WARNING @ Tue, 16 Jun 2020 08:59:58: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Tue, 16 Jun 2020 08:59:58: start model_add_line... INFO @ Tue, 16 Jun 2020 08:59:58: start X-correlation... INFO @ Tue, 16 Jun 2020 08:59:58: end of X-cor INFO @ Tue, 16 Jun 2020 08:59:58: #2 finished! INFO @ Tue, 16 Jun 2020 08:59:58: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:59:58: #2 alternative fragment length(s) may be 4,50,570 bps INFO @ Tue, 16 Jun 2020 08:59:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.05_model.r WARNING @ Tue, 16 Jun 2020 08:59:58: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:59:58: #2 You may need to consider one of the other alternative d(s): 4,50,570 WARNING @ Tue, 16 Jun 2020 08:59:58: #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 08:59:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:59:58: #3 Pre-compute pvalue-qvalue table... 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 09:00:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.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 09:00:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:00:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:00:07: 1000000 INFO @ Tue, 16 Jun 2020 09:00:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:00:12: 2000000 INFO @ Tue, 16 Jun 2020 09:00:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:00:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:00:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.05_summits.bed INFO @ Tue, 16 Jun 2020 09:00:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (541 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:00:17: 3000000 INFO @ Tue, 16 Jun 2020 09:00:23: 4000000 INFO @ Tue, 16 Jun 2020 09:00:28: 5000000 INFO @ Tue, 16 Jun 2020 09:00:29: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:00:29: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:00:29: #1 total tags in treatment: 5148365 INFO @ Tue, 16 Jun 2020 09:00:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:00:29: #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 09:00:29: #1 tags after filtering in treatment: 5148365 INFO @ Tue, 16 Jun 2020 09:00:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:00:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:00:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:00:29: #2 looking for paired plus/minus strand peaks... 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 09:00:29: #2 number of paired peaks: 446 WARNING @ Tue, 16 Jun 2020 09:00:29: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Tue, 16 Jun 2020 09:00:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:00:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:00:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:00:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:00:29: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:00:29: #2 alternative fragment length(s) may be 4,50,570 bps INFO @ Tue, 16 Jun 2020 09:00:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.10_model.r WARNING @ Tue, 16 Jun 2020 09:00:29: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:00:29: #2 You may need to consider one of the other alternative d(s): 4,50,570 WARNING @ Tue, 16 Jun 2020 09:00:29: #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 09:00:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:00:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:00:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.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 09:00:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:00:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:00:36: 1000000 INFO @ Tue, 16 Jun 2020 09:00:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:00:42: 2000000 INFO @ Tue, 16 Jun 2020 09:00:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:00:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:00:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.10_summits.bed INFO @ Tue, 16 Jun 2020 09:00:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (336 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:00:47: 3000000 INFO @ Tue, 16 Jun 2020 09:00:52: 4000000 INFO @ Tue, 16 Jun 2020 09:00:57: 5000000 INFO @ Tue, 16 Jun 2020 09:00:58: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:00:58: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:00:58: #1 total tags in treatment: 5148365 INFO @ Tue, 16 Jun 2020 09:00:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:00:58: #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 09:00:58: #1 tags after filtering in treatment: 5148365 INFO @ Tue, 16 Jun 2020 09:00:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:00:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:00:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:00:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:00:58: #2 number of paired peaks: 446 WARNING @ Tue, 16 Jun 2020 09:00:58: Fewer paired peaks (446) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 446 pairs to build model! INFO @ Tue, 16 Jun 2020 09:00:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:00:58: start X-correlation... INFO @ Tue, 16 Jun 2020 09:00:58: end of X-cor INFO @ Tue, 16 Jun 2020 09:00:58: #2 finished! INFO @ Tue, 16 Jun 2020 09:00:58: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 09:00:58: #2 alternative fragment length(s) may be 4,50,570 bps INFO @ Tue, 16 Jun 2020 09:00:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.20_model.r WARNING @ Tue, 16 Jun 2020 09:00:58: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:00:58: #2 You may need to consider one of the other alternative d(s): 4,50,570 WARNING @ Tue, 16 Jun 2020 09:00:58: #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 09:00:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:00:58: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:01:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:01:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:01:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:01:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466472/SRX466472.20_summits.bed INFO @ Tue, 16 Jun 2020 09:01:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (143 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。