Job ID = 6368025 SRX = SRX466488 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:50:03 prefetch.2.10.7: 1) Downloading 'SRR1163554'... 2020-06-15T23:50:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:57 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:58 prefetch.2.10.7: 'SRR1163554' is valid 2020-06-15T23:51:58 prefetch.2.10.7: 1) 'SRR1163554' was downloaded successfully Read 8667423 spots for SRR1163554/SRR1163554.sra Written 8667423 spots for SRR1163554/SRR1163554.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:03 8667423 reads; of these: 8667423 (100.00%) were unpaired; of these: 153029 (1.77%) aligned 0 times 7021020 (81.00%) aligned exactly 1 time 1493374 (17.23%) aligned >1 times 98.23% overall alignment rate Time searching: 00:02:04 Overall time: 00:02:04 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] 809272 / 8514394 = 0.0950 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 08:56:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.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 08:56:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:56:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:56:57: 1000000 INFO @ Tue, 16 Jun 2020 08:57:02: 2000000 INFO @ Tue, 16 Jun 2020 08:57:08: 3000000 INFO @ Tue, 16 Jun 2020 08:57:14: 4000000 INFO @ Tue, 16 Jun 2020 08:57:19: 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 @ Tue, 16 Jun 2020 08:57:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.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 08:57:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:57:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:57:25: 6000000 INFO @ Tue, 16 Jun 2020 08:57:28: 1000000 INFO @ Tue, 16 Jun 2020 08:57:32: 7000000 INFO @ Tue, 16 Jun 2020 08:57:35: 2000000 INFO @ Tue, 16 Jun 2020 08:57:36: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:57:36: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:57:36: #1 total tags in treatment: 7705122 INFO @ Tue, 16 Jun 2020 08:57:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:36: #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 08:57:36: #1 tags after filtering in treatment: 7705122 INFO @ Tue, 16 Jun 2020 08:57:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:36: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:37: #2 number of paired peaks: 368 WARNING @ Tue, 16 Jun 2020 08:57:37: 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 08:57:37: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:37: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:37: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:57:37: #2 alternative fragment length(s) may be 4,50,486,514 bps INFO @ Tue, 16 Jun 2020 08:57:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.05_model.r WARNING @ Tue, 16 Jun 2020 08:57:37: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:57:37: #2 You may need to consider one of the other alternative d(s): 4,50,486,514 WARNING @ Tue, 16 Jun 2020 08:57:37: #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 08:57:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:57:42: 3000000 INFO @ Tue, 16 Jun 2020 08:57:49: 4000000 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 08:57:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.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 08:57:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:57:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:57:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:57:55: 5000000 INFO @ Tue, 16 Jun 2020 08:57:58: 1000000 INFO @ Tue, 16 Jun 2020 08:58:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.05_summits.bed INFO @ Tue, 16 Jun 2020 08:58:01: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (615 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:58:02: 6000000 INFO @ Tue, 16 Jun 2020 08:58:04: 2000000 INFO @ Tue, 16 Jun 2020 08:58:10: 7000000 INFO @ Tue, 16 Jun 2020 08:58:11: 3000000 INFO @ Tue, 16 Jun 2020 08:58:15: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:58:15: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:58:15: #1 total tags in treatment: 7705122 INFO @ Tue, 16 Jun 2020 08:58:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:58:15: #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 08:58:15: #1 tags after filtering in treatment: 7705122 INFO @ Tue, 16 Jun 2020 08:58:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:58:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:58:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:58:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:58:15: #2 number of paired peaks: 368 WARNING @ Tue, 16 Jun 2020 08:58:15: 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 08:58:15: start model_add_line... INFO @ Tue, 16 Jun 2020 08:58:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:58:15: end of X-cor INFO @ Tue, 16 Jun 2020 08:58:15: #2 finished! INFO @ Tue, 16 Jun 2020 08:58:15: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:58:15: #2 alternative fragment length(s) may be 4,50,486,514 bps INFO @ Tue, 16 Jun 2020 08:58:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.10_model.r WARNING @ Tue, 16 Jun 2020 08:58:15: #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 08:58:15: #2 You may need to consider one of the other alternative d(s): 4,50,486,514 WARNING @ Tue, 16 Jun 2020 08:58:15: #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 08:58:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:58:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:58:17: 4000000 INFO @ Tue, 16 Jun 2020 08:58:23: 5000000 INFO @ Tue, 16 Jun 2020 08:58:29: 6000000 INFO @ Tue, 16 Jun 2020 08:58:31: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:58:34: 7000000 INFO @ Tue, 16 Jun 2020 08:58:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.10_summits.bed INFO @ Tue, 16 Jun 2020 08:58:38: Done! INFO @ Tue, 16 Jun 2020 08:58:38: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:58:38: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:58:38: #1 total tags in treatment: 7705122 INFO @ Tue, 16 Jun 2020 08:58:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:58:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (376 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:58:39: #1 tags after filtering in treatment: 7705122 INFO @ Tue, 16 Jun 2020 08:58:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:58:39: #1 finished! INFO @ Tue, 16 Jun 2020 08:58:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:58:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:58:39: #2 number of paired peaks: 368 WARNING @ Tue, 16 Jun 2020 08:58:39: 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 08:58:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:58:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:58:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:58:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:58:39: #2 predicted fragment length is 50 bps INFO @ Tue, 16 Jun 2020 08:58:39: #2 alternative fragment length(s) may be 4,50,486,514 bps INFO @ Tue, 16 Jun 2020 08:58:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.20_model.r WARNING @ Tue, 16 Jun 2020 08:58:39: #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 08:58:39: #2 You may need to consider one of the other alternative d(s): 4,50,486,514 WARNING @ Tue, 16 Jun 2020 08:58:39: #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 08:58:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:58:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:58:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:59:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:59:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:59:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466488/SRX466488.20_summits.bed INFO @ Tue, 16 Jun 2020 08:59:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (167 records, 4 fields): 1 millis CompletedMACS2peakCalling