Job ID = 12265464 SRX = SRX4082402 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: 00:32:19 287144898 reads; of these: 287144898 (100.00%) were unpaired; of these: 252721307 (88.01%) aligned 0 times 29933740 (10.42%) aligned exactly 1 time 4489851 (1.56%) aligned >1 times 11.99% overall alignment rate Time searching: 00:32:19 Overall time: 00:32:19 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 16 files... [bam_rmdupse_core] 21944334 / 34423591 = 0.6375 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 07:49:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.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 07:49:00: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:49:00: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:49:07: 1000000 INFO @ Sat, 03 Apr 2021 07:49:14: 2000000 INFO @ Sat, 03 Apr 2021 07:49:21: 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 07:49:28: 4000000 INFO @ Sat, 03 Apr 2021 07:49:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.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 07:49:30: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:49:30: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:49:35: 5000000 INFO @ Sat, 03 Apr 2021 07:49:37: 1000000 INFO @ Sat, 03 Apr 2021 07:49:42: 6000000 INFO @ Sat, 03 Apr 2021 07:49:44: 2000000 INFO @ Sat, 03 Apr 2021 07:49:50: 7000000 INFO @ Sat, 03 Apr 2021 07:49:51: 3000000 INFO @ Sat, 03 Apr 2021 07:49:57: 8000000 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 07:49:58: 4000000 INFO @ Sat, 03 Apr 2021 07:50:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.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 07:50:00: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:50:00: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:50:04: 9000000 INFO @ Sat, 03 Apr 2021 07:50:05: 5000000 INFO @ Sat, 03 Apr 2021 07:50:08: 1000000 INFO @ Sat, 03 Apr 2021 07:50:12: 10000000 INFO @ Sat, 03 Apr 2021 07:50:13: 6000000 INFO @ Sat, 03 Apr 2021 07:50:15: 2000000 INFO @ Sat, 03 Apr 2021 07:50:20: 7000000 INFO @ Sat, 03 Apr 2021 07:50:21: 11000000 INFO @ Sat, 03 Apr 2021 07:50:23: 3000000 INFO @ Sat, 03 Apr 2021 07:50:28: 8000000 INFO @ Sat, 03 Apr 2021 07:50:28: 12000000 INFO @ Sat, 03 Apr 2021 07:50:30: 4000000 INFO @ Sat, 03 Apr 2021 07:50:32: #1 tag size is determined as 46 bps INFO @ Sat, 03 Apr 2021 07:50:32: #1 tag size = 46 INFO @ Sat, 03 Apr 2021 07:50:32: #1 total tags in treatment: 12479257 INFO @ Sat, 03 Apr 2021 07:50:32: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:50:32: #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 07:50:32: #1 tags after filtering in treatment: 12479257 INFO @ Sat, 03 Apr 2021 07:50:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:50:32: #1 finished! INFO @ Sat, 03 Apr 2021 07:50:32: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:50:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:50:33: #2 number of paired peaks: 1077 INFO @ Sat, 03 Apr 2021 07:50:33: start model_add_line... INFO @ Sat, 03 Apr 2021 07:50:33: start X-correlation... INFO @ Sat, 03 Apr 2021 07:50:33: end of X-cor INFO @ Sat, 03 Apr 2021 07:50:33: #2 finished! INFO @ Sat, 03 Apr 2021 07:50:33: #2 predicted fragment length is 71 bps INFO @ Sat, 03 Apr 2021 07:50:33: #2 alternative fragment length(s) may be 71 bps INFO @ Sat, 03 Apr 2021 07:50:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.05_model.r WARNING @ Sat, 03 Apr 2021 07:50:33: #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 07:50:33: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Sat, 03 Apr 2021 07:50:33: #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 07:50:33: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:50:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:50:35: 9000000 INFO @ Sat, 03 Apr 2021 07:50:37: 5000000 INFO @ Sat, 03 Apr 2021 07:50:42: 10000000 INFO @ Sat, 03 Apr 2021 07:50:44: 6000000 INFO @ Sat, 03 Apr 2021 07:50:50: 11000000 INFO @ Sat, 03 Apr 2021 07:50:52: 7000000 INFO @ Sat, 03 Apr 2021 07:50:57: 12000000 INFO @ Sat, 03 Apr 2021 07:50:58: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:50:59: 8000000 INFO @ Sat, 03 Apr 2021 07:51:00: #1 tag size is determined as 46 bps INFO @ Sat, 03 Apr 2021 07:51:00: #1 tag size = 46 INFO @ Sat, 03 Apr 2021 07:51:00: #1 total tags in treatment: 12479257 INFO @ Sat, 03 Apr 2021 07:51:00: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:51:00: #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 07:51:00: #1 tags after filtering in treatment: 12479257 INFO @ Sat, 03 Apr 2021 07:51:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:51:00: #1 finished! INFO @ Sat, 03 Apr 2021 07:51:00: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:51:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:51:01: #2 number of paired peaks: 1077 INFO @ Sat, 03 Apr 2021 07:51:01: start model_add_line... INFO @ Sat, 03 Apr 2021 07:51:02: start X-correlation... INFO @ Sat, 03 Apr 2021 07:51:02: end of X-cor INFO @ Sat, 03 Apr 2021 07:51:02: #2 finished! INFO @ Sat, 03 Apr 2021 07:51:02: #2 predicted fragment length is 71 bps INFO @ Sat, 03 Apr 2021 07:51:02: #2 alternative fragment length(s) may be 71 bps INFO @ Sat, 03 Apr 2021 07:51:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.10_model.r WARNING @ Sat, 03 Apr 2021 07:51:02: #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 07:51:02: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Sat, 03 Apr 2021 07:51:02: #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 07:51:02: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:51:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:51:05: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:51:11: 10000000 INFO @ Sat, 03 Apr 2021 07:51:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:51:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:51:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.05_summits.bed INFO @ Sat, 03 Apr 2021 07:51:13: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (15663 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:51:18: 11000000 INFO @ Sat, 03 Apr 2021 07:51:24: 12000000 INFO @ Sat, 03 Apr 2021 07:51:26: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:51:27: #1 tag size is determined as 46 bps INFO @ Sat, 03 Apr 2021 07:51:27: #1 tag size = 46 INFO @ Sat, 03 Apr 2021 07:51:27: #1 total tags in treatment: 12479257 INFO @ Sat, 03 Apr 2021 07:51:27: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:51:27: #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 07:51:27: #1 tags after filtering in treatment: 12479257 INFO @ Sat, 03 Apr 2021 07:51:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:51:27: #1 finished! INFO @ Sat, 03 Apr 2021 07:51:27: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:51:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:51:28: #2 number of paired peaks: 1077 INFO @ Sat, 03 Apr 2021 07:51:28: start model_add_line... INFO @ Sat, 03 Apr 2021 07:51:28: start X-correlation... INFO @ Sat, 03 Apr 2021 07:51:28: end of X-cor INFO @ Sat, 03 Apr 2021 07:51:28: #2 finished! INFO @ Sat, 03 Apr 2021 07:51:28: #2 predicted fragment length is 71 bps INFO @ Sat, 03 Apr 2021 07:51:28: #2 alternative fragment length(s) may be 71 bps INFO @ Sat, 03 Apr 2021 07:51:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.20_model.r WARNING @ Sat, 03 Apr 2021 07:51:28: #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 07:51:28: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Sat, 03 Apr 2021 07:51:28: #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 07:51:28: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:51:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:51:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:51:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:51:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.10_summits.bed INFO @ Sat, 03 Apr 2021 07:51:40: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (9783 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:51:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:52:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:52:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:52:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082402/SRX4082402.20_summits.bed INFO @ Sat, 03 Apr 2021 07:52:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4499 records, 4 fields): 7 millis CompletedMACS2peakCalling