Job ID = 6368378 SRX = SRX495058 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:01:00 prefetch.2.10.7: 1) Downloading 'SRR1198590'... 2020-06-16T00:01:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:02:56 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:02:56 prefetch.2.10.7: 1) 'SRR1198590' was downloaded successfully Read 13809537 spots for SRR1198590/SRR1198590.sra Written 13809537 spots for SRR1198590/SRR1198590.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: 00:02:13 13809537 reads; of these: 13809537 (100.00%) were unpaired; of these: 2268840 (16.43%) aligned 0 times 9710176 (70.32%) aligned exactly 1 time 1830521 (13.26%) aligned >1 times 83.57% overall alignment rate Time searching: 00:02:13 Overall time: 00:02:13 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] 1988304 / 11540697 = 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 09:09:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.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 09:09:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:45: 1000000 INFO @ Tue, 16 Jun 2020 09:09:51: 2000000 INFO @ Tue, 16 Jun 2020 09:09:56: 3000000 INFO @ Tue, 16 Jun 2020 09:10:02: 4000000 INFO @ Tue, 16 Jun 2020 09:10:07: 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 09:10:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.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 09:10:10: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:10: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:13: 6000000 INFO @ Tue, 16 Jun 2020 09:10:16: 1000000 INFO @ Tue, 16 Jun 2020 09:10:18: 7000000 INFO @ Tue, 16 Jun 2020 09:10:21: 2000000 INFO @ Tue, 16 Jun 2020 09:10:24: 8000000 INFO @ Tue, 16 Jun 2020 09:10:27: 3000000 INFO @ Tue, 16 Jun 2020 09:10:30: 9000000 INFO @ Tue, 16 Jun 2020 09:10:33: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:10:33: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:10:33: #1 total tags in treatment: 9552393 INFO @ Tue, 16 Jun 2020 09:10:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:10:33: #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 09:10:33: #1 tags after filtering in treatment: 9552393 INFO @ Tue, 16 Jun 2020 09:10:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:10:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:10:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:10:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:10:33: 4000000 INFO @ Tue, 16 Jun 2020 09:10:34: #2 number of paired peaks: 297 WARNING @ Tue, 16 Jun 2020 09:10:34: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Tue, 16 Jun 2020 09:10:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:10:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:10:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:10:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:10:34: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 09:10:34: #2 alternative fragment length(s) may be 3,40 bps INFO @ Tue, 16 Jun 2020 09:10:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.05_model.r WARNING @ Tue, 16 Jun 2020 09:10:34: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:10:34: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Tue, 16 Jun 2020 09:10:34: #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 09:10:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:10:34: #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 09:10:39: 5000000 INFO @ Tue, 16 Jun 2020 09:10:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.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 09:10:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:44: 6000000 INFO @ Tue, 16 Jun 2020 09:10:45: 1000000 INFO @ Tue, 16 Jun 2020 09:10:50: 7000000 INFO @ Tue, 16 Jun 2020 09:10:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:10:52: 2000000 INFO @ Tue, 16 Jun 2020 09:10:55: 8000000 INFO @ Tue, 16 Jun 2020 09:10:58: 3000000 INFO @ Tue, 16 Jun 2020 09:11:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.05_summits.bed INFO @ Tue, 16 Jun 2020 09:11:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (588 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:01: 9000000 INFO @ Tue, 16 Jun 2020 09:11:04: 4000000 INFO @ Tue, 16 Jun 2020 09:11:04: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:11:04: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:11:04: #1 total tags in treatment: 9552393 INFO @ Tue, 16 Jun 2020 09:11:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:04: #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 09:11:04: #1 tags after filtering in treatment: 9552393 INFO @ Tue, 16 Jun 2020 09:11:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:04: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:05: #2 number of paired peaks: 297 WARNING @ Tue, 16 Jun 2020 09:11:05: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:05: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:05: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 09:11:05: #2 alternative fragment length(s) may be 3,40 bps INFO @ Tue, 16 Jun 2020 09:11:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.10_model.r WARNING @ Tue, 16 Jun 2020 09:11:05: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:05: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Tue, 16 Jun 2020 09:11:05: #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 09:11:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:10: 5000000 INFO @ Tue, 16 Jun 2020 09:11:16: 6000000 INFO @ Tue, 16 Jun 2020 09:11:21: 7000000 INFO @ Tue, 16 Jun 2020 09:11:22: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:27: 8000000 INFO @ Tue, 16 Jun 2020 09:11:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.10_summits.bed INFO @ Tue, 16 Jun 2020 09:11:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (279 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:11:33: 9000000 INFO @ Tue, 16 Jun 2020 09:11:37: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:11:37: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:11:37: #1 total tags in treatment: 9552393 INFO @ Tue, 16 Jun 2020 09:11:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:37: #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 09:11:37: #1 tags after filtering in treatment: 9552393 INFO @ Tue, 16 Jun 2020 09:11:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:11:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:38: #2 number of paired peaks: 297 WARNING @ Tue, 16 Jun 2020 09:11:38: Fewer paired peaks (297) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 297 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:38: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:38: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:38: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:38: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:38: #2 predicted fragment length is 40 bps INFO @ Tue, 16 Jun 2020 09:11:38: #2 alternative fragment length(s) may be 3,40 bps INFO @ Tue, 16 Jun 2020 09:11:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.20_model.r WARNING @ Tue, 16 Jun 2020 09:11:38: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:11:38: #2 You may need to consider one of the other alternative d(s): 3,40 WARNING @ Tue, 16 Jun 2020 09:11:38: #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 09:11:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:55: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:12:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495058/SRX495058.20_summits.bed INFO @ Tue, 16 Jun 2020 09:12:04: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (100 records, 4 fields): 1 millis CompletedMACS2peakCalling