Job ID = 10166078 SRX = SRX8331151 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:19:08 58597521 reads; of these: 58597521 (100.00%) were unpaired; of these: 549679 (0.94%) aligned 0 times 49207194 (83.97%) aligned exactly 1 time 8840648 (15.09%) aligned >1 times 99.06% overall alignment rate Time searching: 00:19:08 Overall time: 00:19:08 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 24 files... [bam_rmdupse_core] 54808531 / 58047842 = 0.9442 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 @ Thu, 08 Oct 2020 20:56:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.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 @ Thu, 08 Oct 2020 20:56:57: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:56:57: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:57:02: 1000000 INFO @ Thu, 08 Oct 2020 20:57:07: 2000000 INFO @ Thu, 08 Oct 2020 20:57:12: 3000000 INFO @ Thu, 08 Oct 2020 20:57:13: #1 tag size is determined as 66 bps INFO @ Thu, 08 Oct 2020 20:57:13: #1 tag size = 66 INFO @ Thu, 08 Oct 2020 20:57:13: #1 total tags in treatment: 3239311 INFO @ Thu, 08 Oct 2020 20:57:13: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:57:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:57:13: #1 tags after filtering in treatment: 3239311 INFO @ Thu, 08 Oct 2020 20:57:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:57:13: #1 finished! INFO @ Thu, 08 Oct 2020 20:57:13: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:57:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:57:14: #2 number of paired peaks: 1486 INFO @ Thu, 08 Oct 2020 20:57:14: start model_add_line... INFO @ Thu, 08 Oct 2020 20:57:14: start X-correlation... INFO @ Thu, 08 Oct 2020 20:57:14: end of X-cor INFO @ Thu, 08 Oct 2020 20:57:14: #2 finished! INFO @ Thu, 08 Oct 2020 20:57:14: #2 predicted fragment length is 68 bps INFO @ Thu, 08 Oct 2020 20:57:14: #2 alternative fragment length(s) may be 68,571,573 bps INFO @ Thu, 08 Oct 2020 20:57:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.05_model.r WARNING @ Thu, 08 Oct 2020 20:57:14: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:57:14: #2 You may need to consider one of the other alternative d(s): 68,571,573 WARNING @ Thu, 08 Oct 2020 20:57:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:57:14: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:57:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:57:21: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:57:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:57:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:57:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.05_summits.bed INFO @ Thu, 08 Oct 2020 20:57:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1984 records, 4 fields): 3 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 @ Thu, 08 Oct 2020 20:57:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.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 @ Thu, 08 Oct 2020 20:57:27: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:57:27: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:57:32: 1000000 INFO @ Thu, 08 Oct 2020 20:57:37: 2000000 INFO @ Thu, 08 Oct 2020 20:57:42: 3000000 INFO @ Thu, 08 Oct 2020 20:57:43: #1 tag size is determined as 66 bps INFO @ Thu, 08 Oct 2020 20:57:43: #1 tag size = 66 INFO @ Thu, 08 Oct 2020 20:57:43: #1 total tags in treatment: 3239311 INFO @ Thu, 08 Oct 2020 20:57:43: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:57:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:57:43: #1 tags after filtering in treatment: 3239311 INFO @ Thu, 08 Oct 2020 20:57:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:57:43: #1 finished! INFO @ Thu, 08 Oct 2020 20:57:43: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:57:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:57:43: #2 number of paired peaks: 1486 INFO @ Thu, 08 Oct 2020 20:57:43: start model_add_line... INFO @ Thu, 08 Oct 2020 20:57:43: start X-correlation... INFO @ Thu, 08 Oct 2020 20:57:43: end of X-cor INFO @ Thu, 08 Oct 2020 20:57:43: #2 finished! INFO @ Thu, 08 Oct 2020 20:57:43: #2 predicted fragment length is 68 bps INFO @ Thu, 08 Oct 2020 20:57:43: #2 alternative fragment length(s) may be 68,571,573 bps INFO @ Thu, 08 Oct 2020 20:57:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.10_model.r WARNING @ Thu, 08 Oct 2020 20:57:43: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:57:43: #2 You may need to consider one of the other alternative d(s): 68,571,573 WARNING @ Thu, 08 Oct 2020 20:57:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:57:43: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:57:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:57:51: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:57:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:57:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:57:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.10_summits.bed INFO @ Thu, 08 Oct 2020 20:57:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (980 records, 4 fields): 3 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 @ Thu, 08 Oct 2020 20:57:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.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 @ Thu, 08 Oct 2020 20:57:57: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:57:57: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:58:02: 1000000 INFO @ Thu, 08 Oct 2020 20:58:07: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:58:12: 3000000 INFO @ Thu, 08 Oct 2020 20:58:13: #1 tag size is determined as 66 bps INFO @ Thu, 08 Oct 2020 20:58:13: #1 tag size = 66 INFO @ Thu, 08 Oct 2020 20:58:13: #1 total tags in treatment: 3239311 INFO @ Thu, 08 Oct 2020 20:58:13: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:58:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:58:13: #1 tags after filtering in treatment: 3239311 INFO @ Thu, 08 Oct 2020 20:58:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:58:13: #1 finished! INFO @ Thu, 08 Oct 2020 20:58:13: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:58:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:58:13: #2 number of paired peaks: 1486 INFO @ Thu, 08 Oct 2020 20:58:13: start model_add_line... INFO @ Thu, 08 Oct 2020 20:58:13: start X-correlation... INFO @ Thu, 08 Oct 2020 20:58:13: end of X-cor INFO @ Thu, 08 Oct 2020 20:58:13: #2 finished! INFO @ Thu, 08 Oct 2020 20:58:13: #2 predicted fragment length is 68 bps INFO @ Thu, 08 Oct 2020 20:58:13: #2 alternative fragment length(s) may be 68,571,573 bps INFO @ Thu, 08 Oct 2020 20:58:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.20_model.r WARNING @ Thu, 08 Oct 2020 20:58:13: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:58:13: #2 You may need to consider one of the other alternative d(s): 68,571,573 WARNING @ Thu, 08 Oct 2020 20:58:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:58:13: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:58:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:58:21: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:58:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:58:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:58:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331151/SRX8331151.20_summits.bed INFO @ Thu, 08 Oct 2020 20:58:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (417 records, 4 fields): 2 millis CompletedMACS2peakCalling