Job ID = 12265158 SRX = SRX4082396 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: 00:08:35 42803340 reads; of these: 42803340 (100.00%) were unpaired; of these: 11590697 (27.08%) aligned 0 times 27601595 (64.48%) aligned exactly 1 time 3611048 (8.44%) aligned >1 times 72.92% overall alignment rate Time searching: 00:08:35 Overall time: 00:08:35 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] 18950290 / 31212643 = 0.6071 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 06:26:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.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 06:26:25: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:26:25: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:26:36: 1000000 INFO @ Sat, 03 Apr 2021 06:26:46: 2000000 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 06:26:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.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 06:26:55: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:26:55: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:26:56: 3000000 INFO @ Sat, 03 Apr 2021 06:27:04: 1000000 INFO @ Sat, 03 Apr 2021 06:27:07: 4000000 INFO @ Sat, 03 Apr 2021 06:27:13: 2000000 INFO @ Sat, 03 Apr 2021 06:27:18: 5000000 INFO @ Sat, 03 Apr 2021 06:27:23: 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 06:27:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.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 06:27:25: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:27:25: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:27:29: 6000000 INFO @ Sat, 03 Apr 2021 06:27:32: 4000000 INFO @ Sat, 03 Apr 2021 06:27:34: 1000000 INFO @ Sat, 03 Apr 2021 06:27:39: 7000000 INFO @ Sat, 03 Apr 2021 06:27:41: 5000000 INFO @ Sat, 03 Apr 2021 06:27:43: 2000000 INFO @ Sat, 03 Apr 2021 06:27:50: 8000000 INFO @ Sat, 03 Apr 2021 06:27:50: 6000000 INFO @ Sat, 03 Apr 2021 06:27:52: 3000000 INFO @ Sat, 03 Apr 2021 06:27:59: 7000000 INFO @ Sat, 03 Apr 2021 06:28:00: 9000000 INFO @ Sat, 03 Apr 2021 06:28:01: 4000000 INFO @ Sat, 03 Apr 2021 06:28:08: 8000000 INFO @ Sat, 03 Apr 2021 06:28:10: 5000000 INFO @ Sat, 03 Apr 2021 06:28:10: 10000000 INFO @ Sat, 03 Apr 2021 06:28:17: 9000000 INFO @ Sat, 03 Apr 2021 06:28:19: 6000000 INFO @ Sat, 03 Apr 2021 06:28:21: 11000000 INFO @ Sat, 03 Apr 2021 06:28:26: 10000000 INFO @ Sat, 03 Apr 2021 06:28:28: 7000000 INFO @ Sat, 03 Apr 2021 06:28:32: 12000000 INFO @ Sat, 03 Apr 2021 06:28:35: #1 tag size is determined as 47 bps INFO @ Sat, 03 Apr 2021 06:28:35: #1 tag size = 47 INFO @ Sat, 03 Apr 2021 06:28:35: #1 total tags in treatment: 12262353 INFO @ Sat, 03 Apr 2021 06:28:35: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:28:35: #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 06:28:35: #1 tags after filtering in treatment: 12262353 INFO @ Sat, 03 Apr 2021 06:28:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:28:35: #1 finished! INFO @ Sat, 03 Apr 2021 06:28:35: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:28:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:28:36: 11000000 INFO @ Sat, 03 Apr 2021 06:28:36: #2 number of paired peaks: 1484 INFO @ Sat, 03 Apr 2021 06:28:36: start model_add_line... INFO @ Sat, 03 Apr 2021 06:28:36: start X-correlation... INFO @ Sat, 03 Apr 2021 06:28:36: end of X-cor INFO @ Sat, 03 Apr 2021 06:28:36: #2 finished! INFO @ Sat, 03 Apr 2021 06:28:36: #2 predicted fragment length is 84 bps INFO @ Sat, 03 Apr 2021 06:28:36: #2 alternative fragment length(s) may be 84 bps INFO @ Sat, 03 Apr 2021 06:28:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.05_model.r WARNING @ Sat, 03 Apr 2021 06:28:36: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:28:36: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sat, 03 Apr 2021 06:28:36: #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 06:28:36: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:28:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:28:37: 8000000 INFO @ Sat, 03 Apr 2021 06:28:45: 12000000 INFO @ Sat, 03 Apr 2021 06:28:47: 9000000 INFO @ Sat, 03 Apr 2021 06:28:48: #1 tag size is determined as 47 bps INFO @ Sat, 03 Apr 2021 06:28:48: #1 tag size = 47 INFO @ Sat, 03 Apr 2021 06:28:48: #1 total tags in treatment: 12262353 INFO @ Sat, 03 Apr 2021 06:28:48: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:28:48: #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 06:28:48: #1 tags after filtering in treatment: 12262353 INFO @ Sat, 03 Apr 2021 06:28:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:28:48: #1 finished! INFO @ Sat, 03 Apr 2021 06:28:48: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:28:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:28:49: #2 number of paired peaks: 1484 INFO @ Sat, 03 Apr 2021 06:28:49: start model_add_line... INFO @ Sat, 03 Apr 2021 06:28:50: start X-correlation... INFO @ Sat, 03 Apr 2021 06:28:50: end of X-cor INFO @ Sat, 03 Apr 2021 06:28:50: #2 finished! INFO @ Sat, 03 Apr 2021 06:28:50: #2 predicted fragment length is 84 bps INFO @ Sat, 03 Apr 2021 06:28:50: #2 alternative fragment length(s) may be 84 bps INFO @ Sat, 03 Apr 2021 06:28:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.10_model.r WARNING @ Sat, 03 Apr 2021 06:28:50: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:28:50: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sat, 03 Apr 2021 06:28:50: #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 06:28:50: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:28:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:28:56: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:29:05: 11000000 INFO @ Sat, 03 Apr 2021 06:29:13: 12000000 INFO @ Sat, 03 Apr 2021 06:29:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:29:15: #1 tag size is determined as 47 bps INFO @ Sat, 03 Apr 2021 06:29:15: #1 tag size = 47 INFO @ Sat, 03 Apr 2021 06:29:15: #1 total tags in treatment: 12262353 INFO @ Sat, 03 Apr 2021 06:29:15: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:29:15: #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 06:29:16: #1 tags after filtering in treatment: 12262353 INFO @ Sat, 03 Apr 2021 06:29:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:29:16: #1 finished! INFO @ Sat, 03 Apr 2021 06:29:16: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:29:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:29:17: #2 number of paired peaks: 1484 INFO @ Sat, 03 Apr 2021 06:29:17: start model_add_line... INFO @ Sat, 03 Apr 2021 06:29:17: start X-correlation... INFO @ Sat, 03 Apr 2021 06:29:17: end of X-cor INFO @ Sat, 03 Apr 2021 06:29:17: #2 finished! INFO @ Sat, 03 Apr 2021 06:29:17: #2 predicted fragment length is 84 bps INFO @ Sat, 03 Apr 2021 06:29:17: #2 alternative fragment length(s) may be 84 bps INFO @ Sat, 03 Apr 2021 06:29:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.20_model.r WARNING @ Sat, 03 Apr 2021 06:29:17: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:29:17: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Sat, 03 Apr 2021 06:29:17: #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 06:29:17: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:29:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:29:25: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:29:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:29:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:29:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.05_summits.bed INFO @ Sat, 03 Apr 2021 06:29:31: Done! pass1 - making usageList (7 chroms): 6 millis pass2 - checking and writing primary data (15977 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:29:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:29:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:29:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.10_summits.bed INFO @ Sat, 03 Apr 2021 06:29:43: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (10964 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:29:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:30:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:30:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:30:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082396/SRX4082396.20_summits.bed INFO @ Sat, 03 Apr 2021 06:30:09: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (5764 records, 4 fields): 24 millis CompletedMACS2peakCalling