Job ID = 10166083 SRX = SRX8331148 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: 00:22:37 63128850 reads; of these: 63128850 (100.00%) were unpaired; of these: 798346 (1.26%) aligned 0 times 52255651 (82.78%) aligned exactly 1 time 10074853 (15.96%) aligned >1 times 98.74% overall alignment rate Time searching: 00:22:37 Overall time: 00:22:37 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 28 files... [bam_rmdupse_core] 51854134 / 62330504 = 0.8319 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 21:04:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.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 21:04:02: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:04:02: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:04:08: 1000000 INFO @ Thu, 08 Oct 2020 21:04:13: 2000000 INFO @ Thu, 08 Oct 2020 21:04:19: 3000000 INFO @ Thu, 08 Oct 2020 21:04:24: 4000000 INFO @ Thu, 08 Oct 2020 21:04:30: 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 @ Thu, 08 Oct 2020 21:04:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.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 21:04:34: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:04:34: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:04:35: 6000000 INFO @ Thu, 08 Oct 2020 21:04:40: 1000000 INFO @ Thu, 08 Oct 2020 21:04:41: 7000000 INFO @ Thu, 08 Oct 2020 21:04:46: 2000000 INFO @ Thu, 08 Oct 2020 21:04:47: 8000000 INFO @ Thu, 08 Oct 2020 21:04:51: 3000000 INFO @ Thu, 08 Oct 2020 21:04:53: 9000000 INFO @ Thu, 08 Oct 2020 21:04:57: 4000000 INFO @ Thu, 08 Oct 2020 21:04:58: 10000000 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 21:05:01: #1 tag size is determined as 65 bps INFO @ Thu, 08 Oct 2020 21:05:01: #1 tag size = 65 INFO @ Thu, 08 Oct 2020 21:05:01: #1 total tags in treatment: 10476370 INFO @ Thu, 08 Oct 2020 21:05:01: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:05:01: #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 21:05:01: #1 tags after filtering in treatment: 10476370 INFO @ Thu, 08 Oct 2020 21:05:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:05:01: #1 finished! INFO @ Thu, 08 Oct 2020 21:05:01: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:05:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:05:02: #2 number of paired peaks: 762 WARNING @ Thu, 08 Oct 2020 21:05:02: Fewer paired peaks (762) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 762 pairs to build model! INFO @ Thu, 08 Oct 2020 21:05:02: start model_add_line... INFO @ Thu, 08 Oct 2020 21:05:02: start X-correlation... INFO @ Thu, 08 Oct 2020 21:05:02: end of X-cor INFO @ Thu, 08 Oct 2020 21:05:02: #2 finished! INFO @ Thu, 08 Oct 2020 21:05:02: #2 predicted fragment length is 55 bps INFO @ Thu, 08 Oct 2020 21:05:02: #2 alternative fragment length(s) may be 3,55 bps INFO @ Thu, 08 Oct 2020 21:05:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.05_model.r WARNING @ Thu, 08 Oct 2020 21:05:02: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:05:02: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Thu, 08 Oct 2020 21:05:02: #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 21:05:02: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:05:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:05:03: 5000000 INFO @ Thu, 08 Oct 2020 21:05:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.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 21:05:04: #1 read tag files... INFO @ Thu, 08 Oct 2020 21:05:04: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 21:05:08: 6000000 INFO @ Thu, 08 Oct 2020 21:05:10: 1000000 INFO @ Thu, 08 Oct 2020 21:05:14: 7000000 INFO @ Thu, 08 Oct 2020 21:05:15: 2000000 INFO @ Thu, 08 Oct 2020 21:05:20: 8000000 INFO @ Thu, 08 Oct 2020 21:05:21: 3000000 INFO @ Thu, 08 Oct 2020 21:05:24: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:05:26: 9000000 INFO @ Thu, 08 Oct 2020 21:05:27: 4000000 INFO @ Thu, 08 Oct 2020 21:05:31: 10000000 INFO @ Thu, 08 Oct 2020 21:05:33: 5000000 INFO @ Thu, 08 Oct 2020 21:05:34: #1 tag size is determined as 65 bps INFO @ Thu, 08 Oct 2020 21:05:34: #1 tag size = 65 INFO @ Thu, 08 Oct 2020 21:05:34: #1 total tags in treatment: 10476370 INFO @ Thu, 08 Oct 2020 21:05:34: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:05:34: #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 21:05:34: #1 tags after filtering in treatment: 10476370 INFO @ Thu, 08 Oct 2020 21:05:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:05:34: #1 finished! INFO @ Thu, 08 Oct 2020 21:05:34: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:05:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 21:05:35: #2 number of paired peaks: 762 WARNING @ Thu, 08 Oct 2020 21:05:35: Fewer paired peaks (762) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 762 pairs to build model! INFO @ Thu, 08 Oct 2020 21:05:35: start model_add_line... INFO @ Thu, 08 Oct 2020 21:05:35: start X-correlation... INFO @ Thu, 08 Oct 2020 21:05:35: end of X-cor INFO @ Thu, 08 Oct 2020 21:05:35: #2 finished! INFO @ Thu, 08 Oct 2020 21:05:35: #2 predicted fragment length is 55 bps INFO @ Thu, 08 Oct 2020 21:05:35: #2 alternative fragment length(s) may be 3,55 bps INFO @ Thu, 08 Oct 2020 21:05:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.10_model.r WARNING @ Thu, 08 Oct 2020 21:05:35: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:05:35: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Thu, 08 Oct 2020 21:05:35: #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 21:05:35: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:05:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:05:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.05_peaks.xls INFO @ Thu, 08 Oct 2020 21:05:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:05:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.05_summits.bed INFO @ Thu, 08 Oct 2020 21:05:35: Done! INFO @ Thu, 08 Oct 2020 21:05:39: 6000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2215 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 21:05:44: 7000000 INFO @ Thu, 08 Oct 2020 21:05:50: 8000000 INFO @ Thu, 08 Oct 2020 21:05:56: 9000000 INFO @ Thu, 08 Oct 2020 21:05:56: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:06:02: 10000000 INFO @ Thu, 08 Oct 2020 21:06:05: #1 tag size is determined as 65 bps INFO @ Thu, 08 Oct 2020 21:06:05: #1 tag size = 65 INFO @ Thu, 08 Oct 2020 21:06:05: #1 total tags in treatment: 10476370 INFO @ Thu, 08 Oct 2020 21:06:05: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 21:06:05: #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 21:06:05: #1 tags after filtering in treatment: 10476370 INFO @ Thu, 08 Oct 2020 21:06:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 21:06:05: #1 finished! INFO @ Thu, 08 Oct 2020 21:06:05: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 21:06:05: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 21:06:06: #2 number of paired peaks: 762 WARNING @ Thu, 08 Oct 2020 21:06:06: Fewer paired peaks (762) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 762 pairs to build model! INFO @ Thu, 08 Oct 2020 21:06:06: start model_add_line... INFO @ Thu, 08 Oct 2020 21:06:06: start X-correlation... INFO @ Thu, 08 Oct 2020 21:06:06: end of X-cor INFO @ Thu, 08 Oct 2020 21:06:06: #2 finished! INFO @ Thu, 08 Oct 2020 21:06:06: #2 predicted fragment length is 55 bps INFO @ Thu, 08 Oct 2020 21:06:06: #2 alternative fragment length(s) may be 3,55 bps INFO @ Thu, 08 Oct 2020 21:06:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.20_model.r WARNING @ Thu, 08 Oct 2020 21:06:06: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 21:06:06: #2 You may need to consider one of the other alternative d(s): 3,55 WARNING @ Thu, 08 Oct 2020 21:06:06: #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 21:06:06: #3 Call peaks... INFO @ Thu, 08 Oct 2020 21:06:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 21:06:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.10_peaks.xls INFO @ Thu, 08 Oct 2020 21:06:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:06:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.10_summits.bed INFO @ Thu, 08 Oct 2020 21:06:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (956 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 21:06:29: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 21:06:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.20_peaks.xls INFO @ Thu, 08 Oct 2020 21:06:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 21:06:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331148/SRX8331148.20_summits.bed INFO @ Thu, 08 Oct 2020 21:06:40: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (366 records, 4 fields): 2 millis CompletedMACS2peakCalling