Job ID = 6368308 SRX = SRX494991 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:02:45 prefetch.2.10.7: 1) Downloading 'SRR1198523'... 2020-06-16T00:02:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:05:24 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:05:24 prefetch.2.10.7: 1) 'SRR1198523' was downloaded successfully Read 13809537 spots for SRR1198523/SRR1198523.sra Written 13809537 spots for SRR1198523/SRR1198523.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: 00:00:01 Multiseed full-index search: 00:02:21 13809537 reads; of these: 13809537 (100.00%) were unpaired; of these: 2268851 (16.43%) aligned 0 times 9710152 (70.31%) aligned exactly 1 time 1830534 (13.26%) aligned >1 times 83.57% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 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] 1988386 / 11540686 = 0.1723 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 09:11:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.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 09:11:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:45: 1000000 INFO @ Tue, 16 Jun 2020 09:11:50: 2000000 INFO @ Tue, 16 Jun 2020 09:11:56: 3000000 INFO @ Tue, 16 Jun 2020 09:12:01: 4000000 INFO @ Tue, 16 Jun 2020 09:12:07: 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 09:12:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.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 09:12:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:12: 6000000 INFO @ Tue, 16 Jun 2020 09:12:15: 1000000 INFO @ Tue, 16 Jun 2020 09:12:18: 7000000 INFO @ Tue, 16 Jun 2020 09:12:21: 2000000 INFO @ Tue, 16 Jun 2020 09:12:24: 8000000 INFO @ Tue, 16 Jun 2020 09:12:27: 3000000 INFO @ Tue, 16 Jun 2020 09:12:29: 9000000 INFO @ Tue, 16 Jun 2020 09:12:33: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:12:33: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:12:33: #1 total tags in treatment: 9552300 INFO @ Tue, 16 Jun 2020 09:12:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:33: #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 09:12:33: #1 tags after filtering in treatment: 9552300 INFO @ Tue, 16 Jun 2020 09:12:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:33: 4000000 INFO @ Tue, 16 Jun 2020 09:12:33: #2 number of paired peaks: 275 WARNING @ Tue, 16 Jun 2020 09:12:33: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:34: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:12:34: #2 alternative fragment length(s) may be 2,45,62,588 bps INFO @ Tue, 16 Jun 2020 09:12:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.05_model.r WARNING @ Tue, 16 Jun 2020 09:12:34: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:12:34: #2 You may need to consider one of the other alternative d(s): 2,45,62,588 WARNING @ Tue, 16 Jun 2020 09:12:34: #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 09:12:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:34: #3 Pre-compute pvalue-qvalue table... 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 09:12:39: 5000000 INFO @ Tue, 16 Jun 2020 09:12:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.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 09:12:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:45: 6000000 INFO @ Tue, 16 Jun 2020 09:12:45: 1000000 INFO @ Tue, 16 Jun 2020 09:12:50: 7000000 INFO @ Tue, 16 Jun 2020 09:12:51: 2000000 INFO @ Tue, 16 Jun 2020 09:12:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:56: 8000000 INFO @ Tue, 16 Jun 2020 09:12:57: 3000000 INFO @ Tue, 16 Jun 2020 09:13:02: 9000000 INFO @ Tue, 16 Jun 2020 09:13:03: 4000000 INFO @ Tue, 16 Jun 2020 09:13:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.05_summits.bed INFO @ Tue, 16 Jun 2020 09:13:05: Done! INFO @ Tue, 16 Jun 2020 09:13:05: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:13:05: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:13:05: #1 total tags in treatment: 9552300 INFO @ Tue, 16 Jun 2020 09:13:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:05: #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 09:13:05: #1 tags after filtering in treatment: 9552300 INFO @ Tue, 16 Jun 2020 09:13:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:13:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:06: #2 number of paired peaks: 275 WARNING @ Tue, 16 Jun 2020 09:13:06: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Tue, 16 Jun 2020 09:13:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:06: start X-correlation... pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (595 records, 4 fields): 3 millis INFO @ Tue, 16 Jun 2020 09:13:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:06: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:13:06: #2 alternative fragment length(s) may be 2,45,62,588 bps INFO @ Tue, 16 Jun 2020 09:13:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.10_model.r CompletedMACS2peakCalling WARNING @ Tue, 16 Jun 2020 09:13:06: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:13:06: #2 You may need to consider one of the other alternative d(s): 2,45,62,588 WARNING @ Tue, 16 Jun 2020 09:13:06: #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 09:13:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:08: 5000000 INFO @ Tue, 16 Jun 2020 09:13:14: 6000000 INFO @ Tue, 16 Jun 2020 09:13:20: 7000000 INFO @ Tue, 16 Jun 2020 09:13:25: 8000000 INFO @ Tue, 16 Jun 2020 09:13:26: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:13:31: 9000000 INFO @ Tue, 16 Jun 2020 09:13:34: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:13:34: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:13:34: #1 total tags in treatment: 9552300 INFO @ Tue, 16 Jun 2020 09:13:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:34: #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 09:13:34: #1 tags after filtering in treatment: 9552300 INFO @ Tue, 16 Jun 2020 09:13:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:13:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:35: #2 number of paired peaks: 275 WARNING @ Tue, 16 Jun 2020 09:13:35: Fewer paired peaks (275) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 275 pairs to build model! INFO @ Tue, 16 Jun 2020 09:13:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:35: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:35: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:35: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:35: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:13:35: #2 alternative fragment length(s) may be 2,45,62,588 bps INFO @ Tue, 16 Jun 2020 09:13:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.20_model.r WARNING @ Tue, 16 Jun 2020 09:13:35: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:13:35: #2 You may need to consider one of the other alternative d(s): 2,45,62,588 WARNING @ Tue, 16 Jun 2020 09:13:35: #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 09:13:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.10_summits.bed INFO @ Tue, 16 Jun 2020 09:13:37: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (298 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:13:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494991/SRX494991.20_summits.bed INFO @ Tue, 16 Jun 2020 09:14:07: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (108 records, 4 fields): 1 millis CompletedMACS2peakCalling