Job ID = 6507867 SRX = SRX494948 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:17:19 prefetch.2.10.7: 1) Downloading 'SRR1198480'... 2020-06-26T13:17:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:18:24 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:18:24 prefetch.2.10.7: 'SRR1198480' is valid 2020-06-26T13:18:24 prefetch.2.10.7: 1) 'SRR1198480' was downloaded successfully Read 13129788 spots for SRR1198480/SRR1198480.sra Written 13129788 spots for SRR1198480/SRR1198480.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: 00:03:08 13129788 reads; of these: 13129788 (100.00%) were unpaired; of these: 270088 (2.06%) aligned 0 times 10628491 (80.95%) aligned exactly 1 time 2231209 (16.99%) aligned >1 times 97.94% overall alignment rate Time searching: 00:03:08 Overall time: 00:03:08 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 8 files... [bam_rmdupse_core] 2051059 / 12859700 = 0.1595 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 @ Fri, 26 Jun 2020 22:25:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.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 @ Fri, 26 Jun 2020 22:25:05: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:25:05: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:25:11: 1000000 INFO @ Fri, 26 Jun 2020 22:25:17: 2000000 INFO @ Fri, 26 Jun 2020 22:25:23: 3000000 INFO @ Fri, 26 Jun 2020 22:25:29: 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 @ Fri, 26 Jun 2020 22:25:34: 5000000 INFO @ Fri, 26 Jun 2020 22:25:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.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 @ Fri, 26 Jun 2020 22:25:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:25:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:25:41: 6000000 INFO @ Fri, 26 Jun 2020 22:25:44: 1000000 INFO @ Fri, 26 Jun 2020 22:25:48: 7000000 INFO @ Fri, 26 Jun 2020 22:25:50: 2000000 INFO @ Fri, 26 Jun 2020 22:25:55: 8000000 INFO @ Fri, 26 Jun 2020 22:25:57: 3000000 INFO @ Fri, 26 Jun 2020 22:26:01: 9000000 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 @ Fri, 26 Jun 2020 22:26:04: 4000000 INFO @ Fri, 26 Jun 2020 22:26:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.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 @ Fri, 26 Jun 2020 22:26:05: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:26:05: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:26:08: 10000000 INFO @ Fri, 26 Jun 2020 22:26:10: 5000000 INFO @ Fri, 26 Jun 2020 22:26:12: 1000000 INFO @ Fri, 26 Jun 2020 22:26:13: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:26:13: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:26:13: #1 total tags in treatment: 10808641 INFO @ Fri, 26 Jun 2020 22:26:13: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:26:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:26:13: #1 tags after filtering in treatment: 10808641 INFO @ Fri, 26 Jun 2020 22:26:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:26:13: #1 finished! INFO @ Fri, 26 Jun 2020 22:26:13: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:26:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:26:14: #2 number of paired peaks: 366 WARNING @ Fri, 26 Jun 2020 22:26:14: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Fri, 26 Jun 2020 22:26:14: start model_add_line... INFO @ Fri, 26 Jun 2020 22:26:14: start X-correlation... INFO @ Fri, 26 Jun 2020 22:26:14: end of X-cor INFO @ Fri, 26 Jun 2020 22:26:14: #2 finished! INFO @ Fri, 26 Jun 2020 22:26:14: #2 predicted fragment length is 48 bps INFO @ Fri, 26 Jun 2020 22:26:14: #2 alternative fragment length(s) may be 2,48,517,539,542 bps INFO @ Fri, 26 Jun 2020 22:26:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.05_model.r WARNING @ Fri, 26 Jun 2020 22:26:14: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:26:14: #2 You may need to consider one of the other alternative d(s): 2,48,517,539,542 WARNING @ Fri, 26 Jun 2020 22:26:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:26:14: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:26:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:26:17: 6000000 INFO @ Fri, 26 Jun 2020 22:26:19: 2000000 INFO @ Fri, 26 Jun 2020 22:26:24: 7000000 INFO @ Fri, 26 Jun 2020 22:26:25: 3000000 INFO @ Fri, 26 Jun 2020 22:26:31: 8000000 INFO @ Fri, 26 Jun 2020 22:26:32: 4000000 INFO @ Fri, 26 Jun 2020 22:26:37: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:26:37: 9000000 INFO @ Fri, 26 Jun 2020 22:26:38: 5000000 INFO @ Fri, 26 Jun 2020 22:26:44: 10000000 INFO @ Fri, 26 Jun 2020 22:26:45: 6000000 INFO @ Fri, 26 Jun 2020 22:26:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:26:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:26:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.05_summits.bed INFO @ Fri, 26 Jun 2020 22:26:48: Done! INFO @ Fri, 26 Jun 2020 22:26:49: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:26:49: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:26:49: #1 total tags in treatment: 10808641 INFO @ Fri, 26 Jun 2020 22:26:49: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:26:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:26:49: #1 tags after filtering in treatment: 10808641 INFO @ Fri, 26 Jun 2020 22:26:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:26:49: #1 finished! INFO @ Fri, 26 Jun 2020 22:26:49: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:26:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:26:50: #2 number of paired peaks: 366 WARNING @ Fri, 26 Jun 2020 22:26:50: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Fri, 26 Jun 2020 22:26:50: start model_add_line... INFO @ Fri, 26 Jun 2020 22:26:50: start X-correlation... INFO @ Fri, 26 Jun 2020 22:26:50: end of X-cor INFO @ Fri, 26 Jun 2020 22:26:50: #2 finished! INFO @ Fri, 26 Jun 2020 22:26:50: #2 predicted fragment length is 48 bps INFO @ Fri, 26 Jun 2020 22:26:50: #2 alternative fragment length(s) may be 2,48,517,539,542 bps INFO @ Fri, 26 Jun 2020 22:26:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.10_model.r WARNING @ Fri, 26 Jun 2020 22:26:50: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:26:50: #2 You may need to consider one of the other alternative d(s): 2,48,517,539,542 WARNING @ Fri, 26 Jun 2020 22:26:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:26:50: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:26:50: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (705 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:26:51: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:26:58: 8000000 INFO @ Fri, 26 Jun 2020 22:27:04: 9000000 INFO @ Fri, 26 Jun 2020 22:27:10: 10000000 INFO @ Fri, 26 Jun 2020 22:27:13: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:27:15: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:27:15: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:27:15: #1 total tags in treatment: 10808641 INFO @ Fri, 26 Jun 2020 22:27:15: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:27:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:27:15: #1 tags after filtering in treatment: 10808641 INFO @ Fri, 26 Jun 2020 22:27:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:27:15: #1 finished! INFO @ Fri, 26 Jun 2020 22:27:15: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:27:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:27:15: #2 number of paired peaks: 366 WARNING @ Fri, 26 Jun 2020 22:27:15: Fewer paired peaks (366) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 366 pairs to build model! INFO @ Fri, 26 Jun 2020 22:27:15: start model_add_line... INFO @ Fri, 26 Jun 2020 22:27:16: start X-correlation... INFO @ Fri, 26 Jun 2020 22:27:16: end of X-cor INFO @ Fri, 26 Jun 2020 22:27:16: #2 finished! INFO @ Fri, 26 Jun 2020 22:27:16: #2 predicted fragment length is 48 bps INFO @ Fri, 26 Jun 2020 22:27:16: #2 alternative fragment length(s) may be 2,48,517,539,542 bps INFO @ Fri, 26 Jun 2020 22:27:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.20_model.r WARNING @ Fri, 26 Jun 2020 22:27:16: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:27:16: #2 You may need to consider one of the other alternative d(s): 2,48,517,539,542 WARNING @ Fri, 26 Jun 2020 22:27:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:27:16: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:27:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:27:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:27:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:27:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.10_summits.bed INFO @ Fri, 26 Jun 2020 22:27:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (477 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:27:39: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:27:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:27:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:27:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494948/SRX494948.20_summits.bed INFO @ Fri, 26 Jun 2020 22:27:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (192 records, 4 fields): 1 millis CompletedMACS2peakCalling