Job ID = 14158370 SRX = SRX7739515 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: 00:03:04 14474984 reads; of these: 14474984 (100.00%) were unpaired; of these: 1311866 (9.06%) aligned 0 times 10972790 (75.81%) aligned exactly 1 time 2190328 (15.13%) aligned >1 times 90.94% overall alignment rate Time searching: 00:03:04 Overall time: 00:03:04 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] 4824567 / 13163118 = 0.3665 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 16:30:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.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 @ Wed, 08 Dec 2021 16:30:20: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:30:20: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:30:25: 1000000 INFO @ Wed, 08 Dec 2021 16:30:30: 2000000 INFO @ Wed, 08 Dec 2021 16:30:35: 3000000 INFO @ Wed, 08 Dec 2021 16:30:40: 4000000 INFO @ Wed, 08 Dec 2021 16:30:45: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 16:30:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.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 @ Wed, 08 Dec 2021 16:30:50: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:30:50: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:30:50: 6000000 INFO @ Wed, 08 Dec 2021 16:30:55: 1000000 INFO @ Wed, 08 Dec 2021 16:30:56: 7000000 INFO @ Wed, 08 Dec 2021 16:31:01: 2000000 INFO @ Wed, 08 Dec 2021 16:31:01: 8000000 INFO @ Wed, 08 Dec 2021 16:31:03: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 16:31:03: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 16:31:03: #1 total tags in treatment: 8338551 INFO @ Wed, 08 Dec 2021 16:31:03: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:31:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 16:31:03: #1 tags after filtering in treatment: 8338551 INFO @ Wed, 08 Dec 2021 16:31:03: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 16:31:03: #1 finished! INFO @ Wed, 08 Dec 2021 16:31:03: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:31:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:31:04: #2 number of paired peaks: 443 WARNING @ Wed, 08 Dec 2021 16:31:04: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Wed, 08 Dec 2021 16:31:04: start model_add_line... INFO @ Wed, 08 Dec 2021 16:31:04: start X-correlation... INFO @ Wed, 08 Dec 2021 16:31:04: end of X-cor INFO @ Wed, 08 Dec 2021 16:31:04: #2 finished! INFO @ Wed, 08 Dec 2021 16:31:04: #2 predicted fragment length is 45 bps INFO @ Wed, 08 Dec 2021 16:31:04: #2 alternative fragment length(s) may be 3,45,516 bps INFO @ Wed, 08 Dec 2021 16:31:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.05_model.r WARNING @ Wed, 08 Dec 2021 16:31:04: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 16:31:04: #2 You may need to consider one of the other alternative d(s): 3,45,516 WARNING @ Wed, 08 Dec 2021 16:31:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 16:31:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:31:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:31:07: 3000000 INFO @ Wed, 08 Dec 2021 16:31:12: 4000000 INFO @ Wed, 08 Dec 2021 16:31:17: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 16:31:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.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 @ Wed, 08 Dec 2021 16:31:20: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:31:20: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:31:20: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:31:23: 6000000 INFO @ Wed, 08 Dec 2021 16:31:25: 1000000 INFO @ Wed, 08 Dec 2021 16:31:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.05_peaks.xls INFO @ Wed, 08 Dec 2021 16:31:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:31:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.05_summits.bed INFO @ Wed, 08 Dec 2021 16:31:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (690 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:31:28: 7000000 INFO @ Wed, 08 Dec 2021 16:31:30: 2000000 INFO @ Wed, 08 Dec 2021 16:31:33: 8000000 INFO @ Wed, 08 Dec 2021 16:31:35: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 16:31:35: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 16:31:35: #1 total tags in treatment: 8338551 INFO @ Wed, 08 Dec 2021 16:31:35: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:31:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 16:31:35: #1 tags after filtering in treatment: 8338551 INFO @ Wed, 08 Dec 2021 16:31:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 16:31:35: #1 finished! INFO @ Wed, 08 Dec 2021 16:31:35: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:31:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:31:36: 3000000 INFO @ Wed, 08 Dec 2021 16:31:36: #2 number of paired peaks: 443 WARNING @ Wed, 08 Dec 2021 16:31:36: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Wed, 08 Dec 2021 16:31:36: start model_add_line... INFO @ Wed, 08 Dec 2021 16:31:36: start X-correlation... INFO @ Wed, 08 Dec 2021 16:31:36: end of X-cor INFO @ Wed, 08 Dec 2021 16:31:36: #2 finished! INFO @ Wed, 08 Dec 2021 16:31:36: #2 predicted fragment length is 45 bps INFO @ Wed, 08 Dec 2021 16:31:36: #2 alternative fragment length(s) may be 3,45,516 bps INFO @ Wed, 08 Dec 2021 16:31:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.10_model.r WARNING @ Wed, 08 Dec 2021 16:31:36: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 16:31:36: #2 You may need to consider one of the other alternative d(s): 3,45,516 WARNING @ Wed, 08 Dec 2021 16:31:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 16:31:36: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:31:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:31:41: 4000000 INFO @ Wed, 08 Dec 2021 16:31:46: 5000000 INFO @ Wed, 08 Dec 2021 16:31:51: 6000000 INFO @ Wed, 08 Dec 2021 16:31:52: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 16:31:56: 7000000 INFO @ Wed, 08 Dec 2021 16:32:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.10_peaks.xls INFO @ Wed, 08 Dec 2021 16:32:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:32:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.10_summits.bed INFO @ Wed, 08 Dec 2021 16:32:00: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (470 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:32:01: 8000000 INFO @ Wed, 08 Dec 2021 16:32:03: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 16:32:03: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 16:32:03: #1 total tags in treatment: 8338551 INFO @ Wed, 08 Dec 2021 16:32:03: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:32:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 16:32:03: #1 tags after filtering in treatment: 8338551 INFO @ Wed, 08 Dec 2021 16:32:03: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 16:32:03: #1 finished! INFO @ Wed, 08 Dec 2021 16:32:03: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:32:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:32:03: #2 number of paired peaks: 443 WARNING @ Wed, 08 Dec 2021 16:32:03: Fewer paired peaks (443) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 443 pairs to build model! INFO @ Wed, 08 Dec 2021 16:32:03: start model_add_line... INFO @ Wed, 08 Dec 2021 16:32:03: start X-correlation... INFO @ Wed, 08 Dec 2021 16:32:03: end of X-cor INFO @ Wed, 08 Dec 2021 16:32:03: #2 finished! INFO @ Wed, 08 Dec 2021 16:32:03: #2 predicted fragment length is 45 bps INFO @ Wed, 08 Dec 2021 16:32:03: #2 alternative fragment length(s) may be 3,45,516 bps INFO @ Wed, 08 Dec 2021 16:32:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.20_model.r WARNING @ Wed, 08 Dec 2021 16:32:03: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 16:32:03: #2 You may need to consider one of the other alternative d(s): 3,45,516 WARNING @ Wed, 08 Dec 2021 16:32:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 16:32:03: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:32:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 16:32:19: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:32:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.20_peaks.xls INFO @ Wed, 08 Dec 2021 16:32:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:32:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7739515/SRX7739515.20_summits.bed INFO @ Wed, 08 Dec 2021 16:32:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (199 records, 4 fields): 2 millis CompletedMACS2peakCalling