Job ID = 14160773 SRX = SRX11322240 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: 00:10:17 12775307 reads; of these: 12775307 (100.00%) were unpaired; of these: 4237957 (33.17%) aligned 0 times 7309718 (57.22%) aligned exactly 1 time 1227632 (9.61%) aligned >1 times 66.83% overall alignment rate Time searching: 00:10:18 Overall time: 00:10:18 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] 1597672 / 8537350 = 0.1871 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 @ Thu, 09 Dec 2021 04:23:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.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, 09 Dec 2021 04:23:53: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:23:53: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:24:07: 1000000 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 @ Thu, 09 Dec 2021 04:24:21: 2000000 INFO @ Thu, 09 Dec 2021 04:24:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.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, 09 Dec 2021 04:24:24: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:24:24: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:24:35: 3000000 INFO @ Thu, 09 Dec 2021 04:24:38: 1000000 INFO @ Thu, 09 Dec 2021 04:24:50: 4000000 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 @ Thu, 09 Dec 2021 04:24:50: 2000000 INFO @ Thu, 09 Dec 2021 04:24:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.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, 09 Dec 2021 04:24:53: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:24:53: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:25:04: 3000000 INFO @ Thu, 09 Dec 2021 04:25:06: 5000000 INFO @ Thu, 09 Dec 2021 04:25:07: 1000000 INFO @ Thu, 09 Dec 2021 04:25:18: 4000000 INFO @ Thu, 09 Dec 2021 04:25:21: 6000000 INFO @ Thu, 09 Dec 2021 04:25:22: 2000000 INFO @ Thu, 09 Dec 2021 04:25:33: 5000000 INFO @ Thu, 09 Dec 2021 04:25:35: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:25:35: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:25:35: #1 total tags in treatment: 6939678 INFO @ Thu, 09 Dec 2021 04:25:35: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:25:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:25:35: #1 tags after filtering in treatment: 6939678 INFO @ Thu, 09 Dec 2021 04:25:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:25:35: #1 finished! INFO @ Thu, 09 Dec 2021 04:25:35: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:25:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:25:36: #2 number of paired peaks: 376 WARNING @ Thu, 09 Dec 2021 04:25:36: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Thu, 09 Dec 2021 04:25:36: start model_add_line... INFO @ Thu, 09 Dec 2021 04:25:36: start X-correlation... INFO @ Thu, 09 Dec 2021 04:25:36: end of X-cor INFO @ Thu, 09 Dec 2021 04:25:36: #2 finished! INFO @ Thu, 09 Dec 2021 04:25:36: #2 predicted fragment length is 142 bps INFO @ Thu, 09 Dec 2021 04:25:36: #2 alternative fragment length(s) may be 142 bps INFO @ Thu, 09 Dec 2021 04:25:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.05_model.r WARNING @ Thu, 09 Dec 2021 04:25:36: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:25:36: #2 You may need to consider one of the other alternative d(s): 142 WARNING @ Thu, 09 Dec 2021 04:25:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:25:36: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:25:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:25:37: 3000000 INFO @ Thu, 09 Dec 2021 04:25:47: 6000000 INFO @ Thu, 09 Dec 2021 04:25:51: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:25:51: 4000000 INFO @ Thu, 09 Dec 2021 04:25:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:25:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:25:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.05_summits.bed INFO @ Thu, 09 Dec 2021 04:25:59: Done! INFO @ Thu, 09 Dec 2021 04:26:00: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:26:00: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:26:00: #1 total tags in treatment: 6939678 INFO @ Thu, 09 Dec 2021 04:26:00: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:26:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (441 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:26:00: #1 tags after filtering in treatment: 6939678 INFO @ Thu, 09 Dec 2021 04:26:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:26:00: #1 finished! INFO @ Thu, 09 Dec 2021 04:26:00: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:26:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:26:00: #2 number of paired peaks: 376 WARNING @ Thu, 09 Dec 2021 04:26:00: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Thu, 09 Dec 2021 04:26:00: start model_add_line... INFO @ Thu, 09 Dec 2021 04:26:01: start X-correlation... INFO @ Thu, 09 Dec 2021 04:26:01: end of X-cor INFO @ Thu, 09 Dec 2021 04:26:01: #2 finished! INFO @ Thu, 09 Dec 2021 04:26:01: #2 predicted fragment length is 142 bps INFO @ Thu, 09 Dec 2021 04:26:01: #2 alternative fragment length(s) may be 142 bps INFO @ Thu, 09 Dec 2021 04:26:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.10_model.r WARNING @ Thu, 09 Dec 2021 04:26:01: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:26:01: #2 You may need to consider one of the other alternative d(s): 142 WARNING @ Thu, 09 Dec 2021 04:26:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:26:01: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:26:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:26:04: 5000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:26:15: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:26:16: 6000000 INFO @ Thu, 09 Dec 2021 04:26:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:26:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:26:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.10_summits.bed INFO @ Thu, 09 Dec 2021 04:26:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (317 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:26:27: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 04:26:27: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 04:26:27: #1 total tags in treatment: 6939678 INFO @ Thu, 09 Dec 2021 04:26:27: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:26:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:26:27: #1 tags after filtering in treatment: 6939678 INFO @ Thu, 09 Dec 2021 04:26:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:26:27: #1 finished! INFO @ Thu, 09 Dec 2021 04:26:27: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:26:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:26:28: #2 number of paired peaks: 376 WARNING @ Thu, 09 Dec 2021 04:26:28: Fewer paired peaks (376) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 376 pairs to build model! INFO @ Thu, 09 Dec 2021 04:26:28: start model_add_line... INFO @ Thu, 09 Dec 2021 04:26:28: start X-correlation... INFO @ Thu, 09 Dec 2021 04:26:28: end of X-cor INFO @ Thu, 09 Dec 2021 04:26:28: #2 finished! INFO @ Thu, 09 Dec 2021 04:26:28: #2 predicted fragment length is 142 bps INFO @ Thu, 09 Dec 2021 04:26:28: #2 alternative fragment length(s) may be 142 bps INFO @ Thu, 09 Dec 2021 04:26:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.20_model.r WARNING @ Thu, 09 Dec 2021 04:26:28: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:26:28: #2 You may need to consider one of the other alternative d(s): 142 WARNING @ Thu, 09 Dec 2021 04:26:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:26:28: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:26:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:26:42: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:26:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:26:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:26:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX11322240/SRX11322240.20_summits.bed INFO @ Thu, 09 Dec 2021 04:26:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (212 records, 4 fields): 2 millis CompletedMACS2peakCalling