Job ID = 16434871 SRX = SRX10435511 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: 00:04:06 11456007 reads; of these: 11456007 (100.00%) were unpaired; of these: 2140932 (18.69%) aligned 0 times 7744229 (67.60%) aligned exactly 1 time 1570846 (13.71%) aligned >1 times 81.31% overall alignment rate Time searching: 00:04:06 Overall time: 00:04:06 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_rmdupse_core] 1029366 / 9315075 = 0.1105 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:13:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.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, 02 Aug 2022 10:13:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:13:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:13:55: 1000000 INFO @ Tue, 02 Aug 2022 10:14:00: 2000000 INFO @ Tue, 02 Aug 2022 10:14:05: 3000000 INFO @ Tue, 02 Aug 2022 10:14:10: 4000000 INFO @ Tue, 02 Aug 2022 10:14:16: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:14:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.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, 02 Aug 2022 10:14:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:14:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:14:21: 6000000 INFO @ Tue, 02 Aug 2022 10:14:24: 1000000 INFO @ Tue, 02 Aug 2022 10:14:27: 7000000 INFO @ Tue, 02 Aug 2022 10:14:30: 2000000 INFO @ Tue, 02 Aug 2022 10:14:33: 8000000 INFO @ Tue, 02 Aug 2022 10:14:34: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:14:34: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:14:34: #1 total tags in treatment: 8285709 INFO @ Tue, 02 Aug 2022 10:14:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:14:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:14:34: #1 tags after filtering in treatment: 8285709 INFO @ Tue, 02 Aug 2022 10:14:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:14:34: #1 finished! INFO @ Tue, 02 Aug 2022 10:14:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:14:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:14:35: #2 number of paired peaks: 502 WARNING @ Tue, 02 Aug 2022 10:14:35: Fewer paired peaks (502) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 502 pairs to build model! INFO @ Tue, 02 Aug 2022 10:14:35: start model_add_line... INFO @ Tue, 02 Aug 2022 10:14:35: start X-correlation... INFO @ Tue, 02 Aug 2022 10:14:35: end of X-cor INFO @ Tue, 02 Aug 2022 10:14:35: #2 finished! INFO @ Tue, 02 Aug 2022 10:14:35: #2 predicted fragment length is 127 bps INFO @ Tue, 02 Aug 2022 10:14:35: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 02 Aug 2022 10:14:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.05_model.r WARNING @ Tue, 02 Aug 2022 10:14:35: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:14:35: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Tue, 02 Aug 2022 10:14:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:14:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:14:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:14:36: 3000000 INFO @ Tue, 02 Aug 2022 10:14:41: 4000000 BedGraph に変換中... INFO @ Tue, 02 Aug 2022 10:14:46: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:14:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.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, 02 Aug 2022 10:14:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:14:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:14:52: 6000000 INFO @ Tue, 02 Aug 2022 10:14:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:14:54: 1000000 INFO @ Tue, 02 Aug 2022 10:14:58: 7000000 INFO @ Tue, 02 Aug 2022 10:15:00: 2000000 INFO @ Tue, 02 Aug 2022 10:15:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:15:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:15:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.05_summits.bed INFO @ Tue, 02 Aug 2022 10:15:02: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1657 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:15:03: 8000000 INFO @ Tue, 02 Aug 2022 10:15:05: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:15:05: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:15:05: #1 total tags in treatment: 8285709 INFO @ Tue, 02 Aug 2022 10:15:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:15:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:15:05: #1 tags after filtering in treatment: 8285709 INFO @ Tue, 02 Aug 2022 10:15:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:15:05: #1 finished! INFO @ Tue, 02 Aug 2022 10:15:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:15:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:15:05: #2 number of paired peaks: 502 WARNING @ Tue, 02 Aug 2022 10:15:05: Fewer paired peaks (502) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 502 pairs to build model! INFO @ Tue, 02 Aug 2022 10:15:05: start model_add_line... INFO @ Tue, 02 Aug 2022 10:15:05: start X-correlation... INFO @ Tue, 02 Aug 2022 10:15:05: end of X-cor INFO @ Tue, 02 Aug 2022 10:15:05: #2 finished! INFO @ Tue, 02 Aug 2022 10:15:05: #2 predicted fragment length is 127 bps INFO @ Tue, 02 Aug 2022 10:15:05: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 02 Aug 2022 10:15:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.10_model.r WARNING @ Tue, 02 Aug 2022 10:15:06: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:15:06: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Tue, 02 Aug 2022 10:15:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:15:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:15:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:15:06: 3000000 INFO @ Tue, 02 Aug 2022 10:15:11: 4000000 INFO @ Tue, 02 Aug 2022 10:15:16: 5000000 INFO @ Tue, 02 Aug 2022 10:15:22: 6000000 INFO @ Tue, 02 Aug 2022 10:15:22: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:15:27: 7000000 INFO @ Tue, 02 Aug 2022 10:15:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:15:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:15:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.10_summits.bed INFO @ Tue, 02 Aug 2022 10:15:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1010 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:15:32: 8000000 INFO @ Tue, 02 Aug 2022 10:15:34: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:15:34: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:15:34: #1 total tags in treatment: 8285709 INFO @ Tue, 02 Aug 2022 10:15:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:15:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:15:34: #1 tags after filtering in treatment: 8285709 INFO @ Tue, 02 Aug 2022 10:15:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:15:34: #1 finished! INFO @ Tue, 02 Aug 2022 10:15:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:15:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:15:34: #2 number of paired peaks: 502 WARNING @ Tue, 02 Aug 2022 10:15:34: Fewer paired peaks (502) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 502 pairs to build model! INFO @ Tue, 02 Aug 2022 10:15:34: start model_add_line... INFO @ Tue, 02 Aug 2022 10:15:34: start X-correlation... INFO @ Tue, 02 Aug 2022 10:15:35: end of X-cor INFO @ Tue, 02 Aug 2022 10:15:35: #2 finished! INFO @ Tue, 02 Aug 2022 10:15:35: #2 predicted fragment length is 127 bps INFO @ Tue, 02 Aug 2022 10:15:35: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 02 Aug 2022 10:15:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.20_model.r WARNING @ Tue, 02 Aug 2022 10:15:35: #2 Since the d (127) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:15:35: #2 You may need to consider one of the other alternative d(s): 127 WARNING @ Tue, 02 Aug 2022 10:15:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:15:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:15:35: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:15:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:16:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:16:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:16:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10435511/SRX10435511.20_summits.bed INFO @ Tue, 02 Aug 2022 10:16:01: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (578 records, 4 fields): 18 millis CompletedMACS2peakCalling