Job ID = 12265380 SRX = SRX4082399 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: 00:18:07 155945446 reads; of these: 155945446 (100.00%) were unpaired; of these: 102457475 (65.70%) aligned 0 times 47194559 (30.26%) aligned exactly 1 time 6293412 (4.04%) aligned >1 times 34.30% overall alignment rate Time searching: 00:18:07 Overall time: 00:18:07 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 24 files... [bam_rmdupse_core] 35449550 / 53487971 = 0.6628 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:15:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.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 @ Sat, 03 Apr 2021 07:15:08: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:15:08: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:15:16: 1000000 INFO @ Sat, 03 Apr 2021 07:15:22: 2000000 INFO @ Sat, 03 Apr 2021 07:15:29: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:15:36: 4000000 INFO @ Sat, 03 Apr 2021 07:15:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.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 @ Sat, 03 Apr 2021 07:15:38: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:15:38: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:15:44: 5000000 INFO @ Sat, 03 Apr 2021 07:15:45: 1000000 INFO @ Sat, 03 Apr 2021 07:15:51: 6000000 INFO @ Sat, 03 Apr 2021 07:15:52: 2000000 INFO @ Sat, 03 Apr 2021 07:15:58: 7000000 INFO @ Sat, 03 Apr 2021 07:15:59: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:16:06: 8000000 INFO @ Sat, 03 Apr 2021 07:16:07: 4000000 INFO @ Sat, 03 Apr 2021 07:16:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.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 @ Sat, 03 Apr 2021 07:16:08: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:16:08: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:16:14: 9000000 INFO @ Sat, 03 Apr 2021 07:16:14: 5000000 INFO @ Sat, 03 Apr 2021 07:16:16: 1000000 INFO @ Sat, 03 Apr 2021 07:16:21: 6000000 INFO @ Sat, 03 Apr 2021 07:16:21: 10000000 INFO @ Sat, 03 Apr 2021 07:16:24: 2000000 INFO @ Sat, 03 Apr 2021 07:16:29: 7000000 INFO @ Sat, 03 Apr 2021 07:16:29: 11000000 INFO @ Sat, 03 Apr 2021 07:16:32: 3000000 INFO @ Sat, 03 Apr 2021 07:16:36: 8000000 INFO @ Sat, 03 Apr 2021 07:16:37: 12000000 INFO @ Sat, 03 Apr 2021 07:16:40: 4000000 INFO @ Sat, 03 Apr 2021 07:16:44: 9000000 INFO @ Sat, 03 Apr 2021 07:16:45: 13000000 INFO @ Sat, 03 Apr 2021 07:16:48: 5000000 INFO @ Sat, 03 Apr 2021 07:16:51: 10000000 INFO @ Sat, 03 Apr 2021 07:16:53: 14000000 INFO @ Sat, 03 Apr 2021 07:16:56: 6000000 INFO @ Sat, 03 Apr 2021 07:16:59: 11000000 INFO @ Sat, 03 Apr 2021 07:17:01: 15000000 INFO @ Sat, 03 Apr 2021 07:17:04: 7000000 INFO @ Sat, 03 Apr 2021 07:17:06: 12000000 INFO @ Sat, 03 Apr 2021 07:17:09: 16000000 INFO @ Sat, 03 Apr 2021 07:17:12: 8000000 INFO @ Sat, 03 Apr 2021 07:17:14: 13000000 INFO @ Sat, 03 Apr 2021 07:17:17: 17000000 INFO @ Sat, 03 Apr 2021 07:17:21: 9000000 INFO @ Sat, 03 Apr 2021 07:17:21: 14000000 INFO @ Sat, 03 Apr 2021 07:17:25: 18000000 INFO @ Sat, 03 Apr 2021 07:17:25: #1 tag size is determined as 48 bps INFO @ Sat, 03 Apr 2021 07:17:25: #1 tag size = 48 INFO @ Sat, 03 Apr 2021 07:17:25: #1 total tags in treatment: 18038421 INFO @ Sat, 03 Apr 2021 07:17:25: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:17:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:17:26: #1 tags after filtering in treatment: 18038421 INFO @ Sat, 03 Apr 2021 07:17:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:17:26: #1 finished! INFO @ Sat, 03 Apr 2021 07:17:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:17:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:17:27: #2 number of paired peaks: 499 WARNING @ Sat, 03 Apr 2021 07:17:27: Fewer paired peaks (499) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 499 pairs to build model! INFO @ Sat, 03 Apr 2021 07:17:27: start model_add_line... INFO @ Sat, 03 Apr 2021 07:17:27: start X-correlation... INFO @ Sat, 03 Apr 2021 07:17:27: end of X-cor INFO @ Sat, 03 Apr 2021 07:17:27: #2 finished! INFO @ Sat, 03 Apr 2021 07:17:27: #2 predicted fragment length is 71 bps INFO @ Sat, 03 Apr 2021 07:17:27: #2 alternative fragment length(s) may be 71 bps INFO @ Sat, 03 Apr 2021 07:17:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.05_model.r WARNING @ Sat, 03 Apr 2021 07:17:27: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:17:27: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Sat, 03 Apr 2021 07:17:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:17:27: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:17:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:17:28: 15000000 INFO @ Sat, 03 Apr 2021 07:17:28: 10000000 INFO @ Sat, 03 Apr 2021 07:17:35: 16000000 INFO @ Sat, 03 Apr 2021 07:17:36: 11000000 INFO @ Sat, 03 Apr 2021 07:17:42: 17000000 INFO @ Sat, 03 Apr 2021 07:17:44: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:17:49: 18000000 INFO @ Sat, 03 Apr 2021 07:17:49: #1 tag size is determined as 48 bps INFO @ Sat, 03 Apr 2021 07:17:49: #1 tag size = 48 INFO @ Sat, 03 Apr 2021 07:17:49: #1 total tags in treatment: 18038421 INFO @ Sat, 03 Apr 2021 07:17:49: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:17:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:17:49: #1 tags after filtering in treatment: 18038421 INFO @ Sat, 03 Apr 2021 07:17:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:17:49: #1 finished! INFO @ Sat, 03 Apr 2021 07:17:49: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:17:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:17:50: #2 number of paired peaks: 499 WARNING @ Sat, 03 Apr 2021 07:17:50: Fewer paired peaks (499) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 499 pairs to build model! INFO @ Sat, 03 Apr 2021 07:17:50: start model_add_line... INFO @ Sat, 03 Apr 2021 07:17:51: start X-correlation... INFO @ Sat, 03 Apr 2021 07:17:51: end of X-cor INFO @ Sat, 03 Apr 2021 07:17:51: #2 finished! INFO @ Sat, 03 Apr 2021 07:17:51: #2 predicted fragment length is 71 bps INFO @ Sat, 03 Apr 2021 07:17:51: #2 alternative fragment length(s) may be 71 bps INFO @ Sat, 03 Apr 2021 07:17:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.10_model.r WARNING @ Sat, 03 Apr 2021 07:17:51: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:17:51: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Sat, 03 Apr 2021 07:17:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:17:51: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:17:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:17:51: 13000000 INFO @ Sat, 03 Apr 2021 07:17:58: 14000000 INFO @ Sat, 03 Apr 2021 07:18:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:18:06: 15000000 INFO @ Sat, 03 Apr 2021 07:18:13: 16000000 INFO @ Sat, 03 Apr 2021 07:18:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:18:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:18:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.05_summits.bed INFO @ Sat, 03 Apr 2021 07:18:19: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (17852 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:18:21: 17000000 INFO @ Sat, 03 Apr 2021 07:18:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:18:29: 18000000 INFO @ Sat, 03 Apr 2021 07:18:29: #1 tag size is determined as 48 bps INFO @ Sat, 03 Apr 2021 07:18:29: #1 tag size = 48 INFO @ Sat, 03 Apr 2021 07:18:29: #1 total tags in treatment: 18038421 INFO @ Sat, 03 Apr 2021 07:18:29: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:18:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:18:29: #1 tags after filtering in treatment: 18038421 INFO @ Sat, 03 Apr 2021 07:18:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:18:29: #1 finished! INFO @ Sat, 03 Apr 2021 07:18:29: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:18:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:18:31: #2 number of paired peaks: 499 WARNING @ Sat, 03 Apr 2021 07:18:31: Fewer paired peaks (499) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 499 pairs to build model! INFO @ Sat, 03 Apr 2021 07:18:31: start model_add_line... INFO @ Sat, 03 Apr 2021 07:18:31: start X-correlation... INFO @ Sat, 03 Apr 2021 07:18:31: end of X-cor INFO @ Sat, 03 Apr 2021 07:18:31: #2 finished! INFO @ Sat, 03 Apr 2021 07:18:31: #2 predicted fragment length is 71 bps INFO @ Sat, 03 Apr 2021 07:18:31: #2 alternative fragment length(s) may be 71 bps INFO @ Sat, 03 Apr 2021 07:18:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.20_model.r WARNING @ Sat, 03 Apr 2021 07:18:31: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:18:31: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Sat, 03 Apr 2021 07:18:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:18:31: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:18:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:18:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:18:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:18:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.10_summits.bed INFO @ Sat, 03 Apr 2021 07:18:43: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (11669 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:19:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:19:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:19:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:19:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082399/SRX4082399.20_summits.bed INFO @ Sat, 03 Apr 2021 07:19:21: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (5162 records, 4 fields): 23 millis CompletedMACS2peakCalling