Job ID = 6368236 SRX = SRX494919 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:10:50 prefetch.2.10.7: 1) Downloading 'SRR1198451'... 2020-06-16T00:10:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:14:10 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:14:10 prefetch.2.10.7: 1) 'SRR1198451' was downloaded successfully Read 22919297 spots for SRR1198451/SRR1198451.sra Written 22919297 spots for SRR1198451/SRR1198451.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: 00:03:53 22919297 reads; of these: 22919297 (100.00%) were unpaired; of these: 10578080 (46.15%) aligned 0 times 10179198 (44.41%) aligned exactly 1 time 2162019 (9.43%) aligned >1 times 53.85% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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] 11437622 / 12341217 = 0.9268 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 09:21:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.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 09:21:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:21:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:21:34: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:21:34: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:21:34: #1 total tags in treatment: 903595 INFO @ Tue, 16 Jun 2020 09:21:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:34: #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 09:21:34: #1 tags after filtering in treatment: 903595 INFO @ Tue, 16 Jun 2020 09:21:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:21:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:34: #2 number of paired peaks: 1658 INFO @ Tue, 16 Jun 2020 09:21:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:34: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:21:34: #2 alternative fragment length(s) may be 51,527,550 bps INFO @ Tue, 16 Jun 2020 09:21:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.05_model.r WARNING @ Tue, 16 Jun 2020 09:21:34: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:21:34: #2 You may need to consider one of the other alternative d(s): 51,527,550 WARNING @ Tue, 16 Jun 2020 09:21:34: #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 09:21:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.05_summits.bed INFO @ Tue, 16 Jun 2020 09:21:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (746 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 09:22:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.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 09:22:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:22:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:22:05: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:22:05: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:22:05: #1 total tags in treatment: 903595 INFO @ Tue, 16 Jun 2020 09:22:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:22:05: #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 09:22:05: #1 tags after filtering in treatment: 903595 INFO @ Tue, 16 Jun 2020 09:22:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:22:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:22:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:22:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:22:05: #2 number of paired peaks: 1658 INFO @ Tue, 16 Jun 2020 09:22:05: start model_add_line... INFO @ Tue, 16 Jun 2020 09:22:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:22:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:22:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:22:05: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:22:05: #2 alternative fragment length(s) may be 51,527,550 bps INFO @ Tue, 16 Jun 2020 09:22:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.10_model.r WARNING @ Tue, 16 Jun 2020 09:22:05: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:22:05: #2 You may need to consider one of the other alternative d(s): 51,527,550 WARNING @ Tue, 16 Jun 2020 09:22:05: #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 09:22:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:22:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:22:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:22:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:22:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:22:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.10_summits.bed INFO @ Tue, 16 Jun 2020 09:22:08: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (470 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 09:22:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.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 09:22:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:22:29: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:22:34: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:22:34: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:22:34: #1 total tags in treatment: 903595 INFO @ Tue, 16 Jun 2020 09:22:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:22:34: #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 09:22:34: #1 tags after filtering in treatment: 903595 INFO @ Tue, 16 Jun 2020 09:22:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:22:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:22:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:22:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:22:34: #2 number of paired peaks: 1658 INFO @ Tue, 16 Jun 2020 09:22:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:22:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:22:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:22:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:22:34: #2 predicted fragment length is 51 bps INFO @ Tue, 16 Jun 2020 09:22:34: #2 alternative fragment length(s) may be 51,527,550 bps INFO @ Tue, 16 Jun 2020 09:22:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.20_model.r WARNING @ Tue, 16 Jun 2020 09:22:34: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:22:34: #2 You may need to consider one of the other alternative d(s): 51,527,550 WARNING @ Tue, 16 Jun 2020 09:22:34: #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 09:22:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:22:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:22:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:22:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:22:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:22:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494919/SRX494919.20_summits.bed INFO @ Tue, 16 Jun 2020 09:22:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 1 millis CompletedMACS2peakCalling