Job ID = 6368681 SRX = SRX5402708 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:28:34 prefetch.2.10.7: 1) Downloading 'SRR8602942'... 2020-06-16T00:28:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:32:49 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:32:49 prefetch.2.10.7: 1) 'SRR8602942' was downloaded successfully Read 33352250 spots for SRR8602942/SRR8602942.sra Written 33352250 spots for SRR8602942/SRR8602942.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: 00:07:00 33352250 reads; of these: 33352250 (100.00%) were unpaired; of these: 4339589 (13.01%) aligned 0 times 24788226 (74.32%) aligned exactly 1 time 4224435 (12.67%) aligned >1 times 86.99% overall alignment rate Time searching: 00:07:00 Overall time: 00:07:00 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 12 files... [bam_rmdupse_core] 16144671 / 29012661 = 0.5565 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 09:47:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.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 09:47:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:39: 1000000 INFO @ Tue, 16 Jun 2020 09:47:45: 2000000 INFO @ Tue, 16 Jun 2020 09:47:51: 3000000 INFO @ Tue, 16 Jun 2020 09:47:57: 4000000 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 09:48:03: 5000000 INFO @ Tue, 16 Jun 2020 09:48:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.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 09:48:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:10: 6000000 INFO @ Tue, 16 Jun 2020 09:48:11: 1000000 INFO @ Tue, 16 Jun 2020 09:48:17: 7000000 INFO @ Tue, 16 Jun 2020 09:48:18: 2000000 INFO @ Tue, 16 Jun 2020 09:48:24: 8000000 INFO @ Tue, 16 Jun 2020 09:48:25: 3000000 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 09:48:31: 9000000 INFO @ Tue, 16 Jun 2020 09:48:32: 4000000 INFO @ Tue, 16 Jun 2020 09:48:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.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 09:48:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:39: 10000000 INFO @ Tue, 16 Jun 2020 09:48:39: 5000000 INFO @ Tue, 16 Jun 2020 09:48:40: 1000000 INFO @ Tue, 16 Jun 2020 09:48:46: 11000000 INFO @ Tue, 16 Jun 2020 09:48:46: 6000000 INFO @ Tue, 16 Jun 2020 09:48:47: 2000000 INFO @ Tue, 16 Jun 2020 09:48:53: 12000000 INFO @ Tue, 16 Jun 2020 09:48:53: 7000000 INFO @ Tue, 16 Jun 2020 09:48:55: 3000000 INFO @ Tue, 16 Jun 2020 09:48:59: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:48:59: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:48:59: #1 total tags in treatment: 12867990 INFO @ Tue, 16 Jun 2020 09:48:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:59: #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 09:48:59: #1 tags after filtering in treatment: 12867990 INFO @ Tue, 16 Jun 2020 09:48:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:48:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:00: #2 number of paired peaks: 368 WARNING @ Tue, 16 Jun 2020 09:49:00: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Tue, 16 Jun 2020 09:49:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:00: 8000000 INFO @ Tue, 16 Jun 2020 09:49:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:00: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:49:00: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 09:49:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.05_model.r WARNING @ Tue, 16 Jun 2020 09:49:00: #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 09:49:00: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 09:49:00: #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 09:49:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:02: 4000000 INFO @ Tue, 16 Jun 2020 09:49:07: 9000000 INFO @ Tue, 16 Jun 2020 09:49:09: 5000000 INFO @ Tue, 16 Jun 2020 09:49:14: 10000000 INFO @ Tue, 16 Jun 2020 09:49:16: 6000000 INFO @ Tue, 16 Jun 2020 09:49:21: 11000000 INFO @ Tue, 16 Jun 2020 09:49:23: 7000000 INFO @ Tue, 16 Jun 2020 09:49:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:28: 12000000 INFO @ Tue, 16 Jun 2020 09:49:30: 8000000 INFO @ Tue, 16 Jun 2020 09:49:34: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:49:34: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:49:34: #1 total tags in treatment: 12867990 INFO @ Tue, 16 Jun 2020 09:49:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:34: #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 09:49:35: #1 tags after filtering in treatment: 12867990 INFO @ Tue, 16 Jun 2020 09:49:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:35: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:36: #2 number of paired peaks: 368 WARNING @ Tue, 16 Jun 2020 09:49:36: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Tue, 16 Jun 2020 09:49:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:36: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:36: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:36: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:36: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:49:36: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 09:49:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.10_model.r WARNING @ Tue, 16 Jun 2020 09:49:36: #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 09:49:36: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 09:49:36: #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 09:49:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:36: 9000000 INFO @ Tue, 16 Jun 2020 09:49:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.05_summits.bed INFO @ Tue, 16 Jun 2020 09:49:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1802 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:49:43: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:49:49: 11000000 INFO @ Tue, 16 Jun 2020 09:49:55: 12000000 INFO @ Tue, 16 Jun 2020 09:50:00: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:50:00: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:50:00: #1 total tags in treatment: 12867990 INFO @ Tue, 16 Jun 2020 09:50:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:00: #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 09:50:00: #1 tags after filtering in treatment: 12867990 INFO @ Tue, 16 Jun 2020 09:50:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:01: #2 number of paired peaks: 368 WARNING @ Tue, 16 Jun 2020 09:50:01: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Tue, 16 Jun 2020 09:50:01: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:01: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:01: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:01: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:01: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:50:01: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 09:50:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.20_model.r WARNING @ Tue, 16 Jun 2020 09:50:01: #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 09:50:01: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 09:50:01: #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 09:50:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:50:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.10_summits.bed INFO @ Tue, 16 Jun 2020 09:50:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (470 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:50:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402708/SRX5402708.20_summits.bed INFO @ Tue, 16 Jun 2020 09:50:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (187 records, 4 fields): 1 millis CompletedMACS2peakCalling