Job ID = 16436169 SRX = SRX13110380 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: 00:04:39 15220230 reads; of these: 15220230 (100.00%) were unpaired; of these: 1535886 (10.09%) aligned 0 times 11607801 (76.27%) aligned exactly 1 time 2076543 (13.64%) aligned >1 times 89.91% overall alignment rate Time searching: 00:04:39 Overall time: 00:04:39 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] 1505415 / 13684344 = 0.1100 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 11:09:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.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 11:09:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:09:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:09:27: 1000000 INFO @ Tue, 02 Aug 2022 11:09:34: 2000000 INFO @ Tue, 02 Aug 2022 11:09:40: 3000000 INFO @ Tue, 02 Aug 2022 11:09:46: 4000000 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 11:09:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.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 11:09:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:09:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:09:52: 5000000 INFO @ Tue, 02 Aug 2022 11:09:57: 1000000 INFO @ Tue, 02 Aug 2022 11:09:59: 6000000 INFO @ Tue, 02 Aug 2022 11:10:03: 2000000 INFO @ Tue, 02 Aug 2022 11:10:05: 7000000 INFO @ Tue, 02 Aug 2022 11:10:09: 3000000 INFO @ Tue, 02 Aug 2022 11:10:12: 8000000 INFO @ Tue, 02 Aug 2022 11:10:15: 4000000 INFO @ Tue, 02 Aug 2022 11:10:19: 9000000 BedGraph に変換中... 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 11:10:21: 5000000 INFO @ Tue, 02 Aug 2022 11:10:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.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 11:10:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 11:10:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 11:10:25: 10000000 INFO @ Tue, 02 Aug 2022 11:10:27: 6000000 INFO @ Tue, 02 Aug 2022 11:10:28: 1000000 INFO @ Tue, 02 Aug 2022 11:10:32: 11000000 INFO @ Tue, 02 Aug 2022 11:10:33: 7000000 INFO @ Tue, 02 Aug 2022 11:10:35: 2000000 INFO @ Tue, 02 Aug 2022 11:10:39: 8000000 INFO @ Tue, 02 Aug 2022 11:10:39: 12000000 INFO @ Tue, 02 Aug 2022 11:10:40: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:10:40: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:10:40: #1 total tags in treatment: 12178929 INFO @ Tue, 02 Aug 2022 11:10:40: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:10:40: #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 11:10:40: #1 tags after filtering in treatment: 12178929 INFO @ Tue, 02 Aug 2022 11:10:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:10:40: #1 finished! INFO @ Tue, 02 Aug 2022 11:10:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:10:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:10:41: #2 number of paired peaks: 234 WARNING @ Tue, 02 Aug 2022 11:10:41: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Tue, 02 Aug 2022 11:10:41: start model_add_line... INFO @ Tue, 02 Aug 2022 11:10:41: start X-correlation... INFO @ Tue, 02 Aug 2022 11:10:41: end of X-cor INFO @ Tue, 02 Aug 2022 11:10:41: #2 finished! INFO @ Tue, 02 Aug 2022 11:10:41: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 11:10:41: #2 alternative fragment length(s) may be 4,73 bps INFO @ Tue, 02 Aug 2022 11:10:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.05_model.r WARNING @ Tue, 02 Aug 2022 11:10:41: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:10:41: #2 You may need to consider one of the other alternative d(s): 4,73 WARNING @ Tue, 02 Aug 2022 11:10:41: #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 11:10:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:10:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:10:42: 3000000 INFO @ Tue, 02 Aug 2022 11:10:45: 9000000 INFO @ Tue, 02 Aug 2022 11:10:48: 4000000 INFO @ Tue, 02 Aug 2022 11:10:50: 10000000 INFO @ Tue, 02 Aug 2022 11:10:55: 5000000 INFO @ Tue, 02 Aug 2022 11:10:56: 11000000 INFO @ Tue, 02 Aug 2022 11:11:01: 6000000 INFO @ Tue, 02 Aug 2022 11:11:02: 12000000 INFO @ Tue, 02 Aug 2022 11:11:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:11:03: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:11:03: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:11:03: #1 total tags in treatment: 12178929 INFO @ Tue, 02 Aug 2022 11:11:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:11:03: #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 11:11:03: #1 tags after filtering in treatment: 12178929 INFO @ Tue, 02 Aug 2022 11:11:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:11:03: #1 finished! INFO @ Tue, 02 Aug 2022 11:11:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:11:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:11:04: #2 number of paired peaks: 234 WARNING @ Tue, 02 Aug 2022 11:11:04: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Tue, 02 Aug 2022 11:11:04: start model_add_line... INFO @ Tue, 02 Aug 2022 11:11:04: start X-correlation... INFO @ Tue, 02 Aug 2022 11:11:04: end of X-cor INFO @ Tue, 02 Aug 2022 11:11:04: #2 finished! INFO @ Tue, 02 Aug 2022 11:11:04: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 11:11:04: #2 alternative fragment length(s) may be 4,73 bps INFO @ Tue, 02 Aug 2022 11:11:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.10_model.r WARNING @ Tue, 02 Aug 2022 11:11:04: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:11:04: #2 You may need to consider one of the other alternative d(s): 4,73 WARNING @ Tue, 02 Aug 2022 11:11:04: #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 11:11:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:11:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 11:11:08: 7000000 INFO @ Tue, 02 Aug 2022 11:11:14: 8000000 INFO @ Tue, 02 Aug 2022 11:11:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.05_peaks.xls INFO @ Tue, 02 Aug 2022 11:11:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:11:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.05_summits.bed INFO @ Tue, 02 Aug 2022 11:11:15: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (602 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 11:11:20: 9000000 INFO @ Tue, 02 Aug 2022 11:11:26: 10000000 INFO @ Tue, 02 Aug 2022 11:11:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:11:32: 11000000 INFO @ Tue, 02 Aug 2022 11:11:38: 12000000 INFO @ Tue, 02 Aug 2022 11:11:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.10_peaks.xls INFO @ Tue, 02 Aug 2022 11:11:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:11:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.10_summits.bed INFO @ Tue, 02 Aug 2022 11:11:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (375 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 11:11:39: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 11:11:39: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 11:11:39: #1 total tags in treatment: 12178929 INFO @ Tue, 02 Aug 2022 11:11:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 11:11:39: #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 11:11:40: #1 tags after filtering in treatment: 12178929 INFO @ Tue, 02 Aug 2022 11:11:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 11:11:40: #1 finished! INFO @ Tue, 02 Aug 2022 11:11:40: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 11:11:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 11:11:40: #2 number of paired peaks: 234 WARNING @ Tue, 02 Aug 2022 11:11:40: Fewer paired peaks (234) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 234 pairs to build model! INFO @ Tue, 02 Aug 2022 11:11:40: start model_add_line... INFO @ Tue, 02 Aug 2022 11:11:40: start X-correlation... INFO @ Tue, 02 Aug 2022 11:11:41: end of X-cor INFO @ Tue, 02 Aug 2022 11:11:41: #2 finished! INFO @ Tue, 02 Aug 2022 11:11:41: #2 predicted fragment length is 73 bps INFO @ Tue, 02 Aug 2022 11:11:41: #2 alternative fragment length(s) may be 4,73 bps INFO @ Tue, 02 Aug 2022 11:11:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.20_model.r WARNING @ Tue, 02 Aug 2022 11:11:41: #2 Since the d (73) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 11:11:41: #2 You may need to consider one of the other alternative d(s): 4,73 WARNING @ Tue, 02 Aug 2022 11:11:41: #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 11:11:41: #3 Call peaks... INFO @ Tue, 02 Aug 2022 11:11:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 11:12:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 11:12:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.20_peaks.xls INFO @ Tue, 02 Aug 2022 11:12:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 11:12:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX13110380/SRX13110380.20_summits.bed INFO @ Tue, 02 Aug 2022 11:12:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (214 records, 4 fields): 20 millis CompletedMACS2peakCalling