Job ID = 12265138 SRX = SRX4082397 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: 00:07:21 39099808 reads; of these: 39099808 (100.00%) were unpaired; of these: 8824560 (22.57%) aligned 0 times 26716158 (68.33%) aligned exactly 1 time 3559090 (9.10%) aligned >1 times 77.43% overall alignment rate Time searching: 00:07:21 Overall time: 00:07:21 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] 16638868 / 30275248 = 0.5496 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 06:22:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.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 06:22:50: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:22:50: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:22:56: 1000000 INFO @ Sat, 03 Apr 2021 06:23:01: 2000000 INFO @ Sat, 03 Apr 2021 06:23:05: 3000000 INFO @ Sat, 03 Apr 2021 06:23:10: 4000000 INFO @ Sat, 03 Apr 2021 06:23:15: 5000000 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 06:23:20: 6000000 INFO @ Sat, 03 Apr 2021 06:23:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.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 06:23:20: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:23:20: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:23:24: 7000000 INFO @ Sat, 03 Apr 2021 06:23:25: 1000000 INFO @ Sat, 03 Apr 2021 06:23:29: 8000000 INFO @ Sat, 03 Apr 2021 06:23:30: 2000000 INFO @ Sat, 03 Apr 2021 06:23:34: 9000000 INFO @ Sat, 03 Apr 2021 06:23:35: 3000000 INFO @ Sat, 03 Apr 2021 06:23:39: 10000000 INFO @ Sat, 03 Apr 2021 06:23:40: 4000000 INFO @ Sat, 03 Apr 2021 06:23:44: 11000000 INFO @ Sat, 03 Apr 2021 06:23:45: 5000000 INFO @ Sat, 03 Apr 2021 06:23:48: 12000000 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 06:23:50: 6000000 INFO @ Sat, 03 Apr 2021 06:23:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.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 06:23:50: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:23:50: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:23:53: 13000000 INFO @ Sat, 03 Apr 2021 06:23:55: 7000000 INFO @ Sat, 03 Apr 2021 06:23:55: 1000000 INFO @ Sat, 03 Apr 2021 06:23:56: #1 tag size is determined as 49 bps INFO @ Sat, 03 Apr 2021 06:23:56: #1 tag size = 49 INFO @ Sat, 03 Apr 2021 06:23:56: #1 total tags in treatment: 13636380 INFO @ Sat, 03 Apr 2021 06:23:56: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:23:56: #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 06:23:57: #1 tags after filtering in treatment: 13636380 INFO @ Sat, 03 Apr 2021 06:23:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:23:57: #1 finished! INFO @ Sat, 03 Apr 2021 06:23:57: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:23:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:23:58: #2 number of paired peaks: 814 WARNING @ Sat, 03 Apr 2021 06:23:58: Fewer paired peaks (814) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 814 pairs to build model! INFO @ Sat, 03 Apr 2021 06:23:58: start model_add_line... INFO @ Sat, 03 Apr 2021 06:23:58: start X-correlation... INFO @ Sat, 03 Apr 2021 06:23:58: end of X-cor INFO @ Sat, 03 Apr 2021 06:23:58: #2 finished! INFO @ Sat, 03 Apr 2021 06:23:58: #2 predicted fragment length is 66 bps INFO @ Sat, 03 Apr 2021 06:23:58: #2 alternative fragment length(s) may be 66 bps INFO @ Sat, 03 Apr 2021 06:23:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.05_model.r WARNING @ Sat, 03 Apr 2021 06:23:58: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:23:58: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sat, 03 Apr 2021 06:23:58: #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 06:23:58: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:23:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:23:59: 8000000 INFO @ Sat, 03 Apr 2021 06:24:00: 2000000 INFO @ Sat, 03 Apr 2021 06:24:04: 9000000 INFO @ Sat, 03 Apr 2021 06:24:05: 3000000 INFO @ Sat, 03 Apr 2021 06:24:09: 10000000 INFO @ Sat, 03 Apr 2021 06:24:10: 4000000 INFO @ Sat, 03 Apr 2021 06:24:14: 11000000 INFO @ Sat, 03 Apr 2021 06:24:15: 5000000 INFO @ Sat, 03 Apr 2021 06:24:19: 12000000 INFO @ Sat, 03 Apr 2021 06:24:19: 6000000 INFO @ Sat, 03 Apr 2021 06:24:23: 13000000 INFO @ Sat, 03 Apr 2021 06:24:24: 7000000 INFO @ Sat, 03 Apr 2021 06:24:26: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:24:27: #1 tag size is determined as 49 bps INFO @ Sat, 03 Apr 2021 06:24:27: #1 tag size = 49 INFO @ Sat, 03 Apr 2021 06:24:27: #1 total tags in treatment: 13636380 INFO @ Sat, 03 Apr 2021 06:24:27: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:24:27: #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 06:24:27: #1 tags after filtering in treatment: 13636380 INFO @ Sat, 03 Apr 2021 06:24:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:24:27: #1 finished! INFO @ Sat, 03 Apr 2021 06:24:27: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:24:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:24:28: #2 number of paired peaks: 814 WARNING @ Sat, 03 Apr 2021 06:24:28: Fewer paired peaks (814) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 814 pairs to build model! INFO @ Sat, 03 Apr 2021 06:24:28: start model_add_line... INFO @ Sat, 03 Apr 2021 06:24:28: start X-correlation... INFO @ Sat, 03 Apr 2021 06:24:28: end of X-cor INFO @ Sat, 03 Apr 2021 06:24:28: #2 finished! INFO @ Sat, 03 Apr 2021 06:24:28: #2 predicted fragment length is 66 bps INFO @ Sat, 03 Apr 2021 06:24:28: #2 alternative fragment length(s) may be 66 bps INFO @ Sat, 03 Apr 2021 06:24:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.10_model.r WARNING @ Sat, 03 Apr 2021 06:24:28: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:24:28: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sat, 03 Apr 2021 06:24:28: #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 06:24:28: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:24:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:24:29: 8000000 INFO @ Sat, 03 Apr 2021 06:24:34: 9000000 INFO @ Sat, 03 Apr 2021 06:24:38: 10000000 INFO @ Sat, 03 Apr 2021 06:24:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:24:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:24:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.05_summits.bed INFO @ Sat, 03 Apr 2021 06:24:41: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (15158 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:24:43: 11000000 INFO @ Sat, 03 Apr 2021 06:24:48: 12000000 INFO @ Sat, 03 Apr 2021 06:24:52: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:24:55: #1 tag size is determined as 49 bps INFO @ Sat, 03 Apr 2021 06:24:55: #1 tag size = 49 INFO @ Sat, 03 Apr 2021 06:24:55: #1 total tags in treatment: 13636380 INFO @ Sat, 03 Apr 2021 06:24:55: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:24:55: #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 06:24:55: #1 tags after filtering in treatment: 13636380 INFO @ Sat, 03 Apr 2021 06:24:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:24:55: #1 finished! INFO @ Sat, 03 Apr 2021 06:24:55: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:24:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:24:56: #2 number of paired peaks: 814 WARNING @ Sat, 03 Apr 2021 06:24:56: Fewer paired peaks (814) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 814 pairs to build model! INFO @ Sat, 03 Apr 2021 06:24:56: start model_add_line... INFO @ Sat, 03 Apr 2021 06:24:57: start X-correlation... INFO @ Sat, 03 Apr 2021 06:24:57: end of X-cor INFO @ Sat, 03 Apr 2021 06:24:57: #2 finished! INFO @ Sat, 03 Apr 2021 06:24:57: #2 predicted fragment length is 66 bps INFO @ Sat, 03 Apr 2021 06:24:57: #2 alternative fragment length(s) may be 66 bps INFO @ Sat, 03 Apr 2021 06:24:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.20_model.r WARNING @ Sat, 03 Apr 2021 06:24:57: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:24:57: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Sat, 03 Apr 2021 06:24:57: #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 06:24:57: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:24:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:24:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:25:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:25:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:25:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.10_summits.bed INFO @ Sat, 03 Apr 2021 06:25:13: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (9340 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:25:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:25:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:25:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:25:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4082397/SRX4082397.20_summits.bed INFO @ Sat, 03 Apr 2021 06:25:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4171 records, 4 fields): 6 millis CompletedMACS2peakCalling