Job ID = 14160713 SRX = SRX10569201 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2021-12-08T18:52:00 prefetch.2.10.7: 1) Downloading 'SRR14202291'... 2021-12-08T18:52:00 prefetch.2.10.7: Downloading via HTTPS... 2021-12-08T18:54:09 prefetch.2.10.7: HTTPS download succeed 2021-12-08T18:54:09 prefetch.2.10.7: 1) 'SRR14202291' was downloaded successfully 2021-12-08T18:54:09 prefetch.2.10.7: 'SRR14202291' has 0 unresolved dependencies Read 22353040 spots for SRR14202291/SRR14202291.sra Written 22353040 spots for SRR14202291/SRR14202291.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160855 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:22 22353040 reads; of these: 22353040 (100.00%) were unpaired; of these: 7259536 (32.48%) aligned 0 times 12577326 (56.27%) aligned exactly 1 time 2516178 (11.26%) aligned >1 times 67.52% overall alignment rate Time searching: 00:07:22 Overall time: 00:07:22 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] 1916776 / 15093504 = 0.1270 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 04:10:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.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 @ Thu, 09 Dec 2021 04:10:02: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:10:02: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:10:13: 1000000 INFO @ Thu, 09 Dec 2021 04:10:24: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 04:10:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.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 @ Thu, 09 Dec 2021 04:10:32: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:10:32: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:10:34: 3000000 INFO @ Thu, 09 Dec 2021 04:10:41: 1000000 INFO @ Thu, 09 Dec 2021 04:10:44: 4000000 INFO @ Thu, 09 Dec 2021 04:10:49: 2000000 INFO @ Thu, 09 Dec 2021 04:10:54: 5000000 INFO @ Thu, 09 Dec 2021 04:10:58: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 04:11:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.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 @ Thu, 09 Dec 2021 04:11:02: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:11:02: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:11:04: 6000000 INFO @ Thu, 09 Dec 2021 04:11:07: 4000000 INFO @ Thu, 09 Dec 2021 04:11:10: 1000000 INFO @ Thu, 09 Dec 2021 04:11:14: 7000000 INFO @ Thu, 09 Dec 2021 04:11:16: 5000000 INFO @ Thu, 09 Dec 2021 04:11:18: 2000000 INFO @ Thu, 09 Dec 2021 04:11:24: 6000000 INFO @ Thu, 09 Dec 2021 04:11:24: 8000000 INFO @ Thu, 09 Dec 2021 04:11:26: 3000000 INFO @ Thu, 09 Dec 2021 04:11:33: 7000000 INFO @ Thu, 09 Dec 2021 04:11:34: 4000000 INFO @ Thu, 09 Dec 2021 04:11:35: 9000000 INFO @ Thu, 09 Dec 2021 04:11:41: 8000000 INFO @ Thu, 09 Dec 2021 04:11:42: 5000000 INFO @ Thu, 09 Dec 2021 04:11:45: 10000000 INFO @ Thu, 09 Dec 2021 04:11:50: 9000000 INFO @ Thu, 09 Dec 2021 04:11:50: 6000000 INFO @ Thu, 09 Dec 2021 04:11:55: 11000000 INFO @ Thu, 09 Dec 2021 04:11:58: 7000000 INFO @ Thu, 09 Dec 2021 04:11:59: 10000000 INFO @ Thu, 09 Dec 2021 04:12:06: 12000000 INFO @ Thu, 09 Dec 2021 04:12:06: 8000000 INFO @ Thu, 09 Dec 2021 04:12:07: 11000000 INFO @ Thu, 09 Dec 2021 04:12:14: 9000000 INFO @ Thu, 09 Dec 2021 04:12:16: 13000000 INFO @ Thu, 09 Dec 2021 04:12:16: 12000000 INFO @ Thu, 09 Dec 2021 04:12:18: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:12:18: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:12:18: #1 total tags in treatment: 13176728 INFO @ Thu, 09 Dec 2021 04:12:18: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:12:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:12:18: #1 tags after filtering in treatment: 13176728 INFO @ Thu, 09 Dec 2021 04:12:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:12:18: #1 finished! INFO @ Thu, 09 Dec 2021 04:12:18: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:12:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:12:19: #2 number of paired peaks: 234 WARNING @ Thu, 09 Dec 2021 04:12:19: 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 @ Thu, 09 Dec 2021 04:12:19: start model_add_line... INFO @ Thu, 09 Dec 2021 04:12:19: start X-correlation... INFO @ Thu, 09 Dec 2021 04:12:19: end of X-cor INFO @ Thu, 09 Dec 2021 04:12:19: #2 finished! INFO @ Thu, 09 Dec 2021 04:12:19: #2 predicted fragment length is 59 bps INFO @ Thu, 09 Dec 2021 04:12:19: #2 alternative fragment length(s) may be 2,59,585 bps INFO @ Thu, 09 Dec 2021 04:12:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.05_model.r WARNING @ Thu, 09 Dec 2021 04:12:19: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:12:19: #2 You may need to consider one of the other alternative d(s): 2,59,585 WARNING @ Thu, 09 Dec 2021 04:12:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:12:19: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:12:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:12:22: 10000000 INFO @ Thu, 09 Dec 2021 04:12:25: 13000000 INFO @ Thu, 09 Dec 2021 04:12:26: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:12:26: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:12:26: #1 total tags in treatment: 13176728 INFO @ Thu, 09 Dec 2021 04:12:26: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:12:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:12:27: #1 tags after filtering in treatment: 13176728 INFO @ Thu, 09 Dec 2021 04:12:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:12:27: #1 finished! INFO @ Thu, 09 Dec 2021 04:12:27: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:12:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:12:28: #2 number of paired peaks: 234 WARNING @ Thu, 09 Dec 2021 04:12:28: 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 @ Thu, 09 Dec 2021 04:12:28: start model_add_line... INFO @ Thu, 09 Dec 2021 04:12:28: start X-correlation... INFO @ Thu, 09 Dec 2021 04:12:28: end of X-cor INFO @ Thu, 09 Dec 2021 04:12:28: #2 finished! INFO @ Thu, 09 Dec 2021 04:12:28: #2 predicted fragment length is 59 bps INFO @ Thu, 09 Dec 2021 04:12:28: #2 alternative fragment length(s) may be 2,59,585 bps INFO @ Thu, 09 Dec 2021 04:12:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.10_model.r WARNING @ Thu, 09 Dec 2021 04:12:28: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:12:28: #2 You may need to consider one of the other alternative d(s): 2,59,585 WARNING @ Thu, 09 Dec 2021 04:12:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:12:28: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:12:28: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:12:30: 11000000 INFO @ Thu, 09 Dec 2021 04:12:37: 12000000 INFO @ Thu, 09 Dec 2021 04:12:45: 13000000 INFO @ Thu, 09 Dec 2021 04:12:47: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:12:47: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:12:47: #1 total tags in treatment: 13176728 INFO @ Thu, 09 Dec 2021 04:12:47: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:12:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 04:12:47: #1 tags after filtering in treatment: 13176728 INFO @ Thu, 09 Dec 2021 04:12:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:12:47: #1 finished! INFO @ Thu, 09 Dec 2021 04:12:47: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:12:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:12:48: #2 number of paired peaks: 234 WARNING @ Thu, 09 Dec 2021 04:12:48: 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 @ Thu, 09 Dec 2021 04:12:48: start model_add_line... INFO @ Thu, 09 Dec 2021 04:12:48: start X-correlation... INFO @ Thu, 09 Dec 2021 04:12:48: end of X-cor INFO @ Thu, 09 Dec 2021 04:12:48: #2 finished! INFO @ Thu, 09 Dec 2021 04:12:48: #2 predicted fragment length is 59 bps INFO @ Thu, 09 Dec 2021 04:12:48: #2 alternative fragment length(s) may be 2,59,585 bps INFO @ Thu, 09 Dec 2021 04:12:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.20_model.r WARNING @ Thu, 09 Dec 2021 04:12:48: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:12:48: #2 You may need to consider one of the other alternative d(s): 2,59,585 WARNING @ Thu, 09 Dec 2021 04:12:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 04:12:48: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:12:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:12:53: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:13:01: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:13:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:13:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:13:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.05_summits.bed INFO @ Thu, 09 Dec 2021 04:13:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (505 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:13:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:13:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:13:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.10_summits.bed INFO @ Thu, 09 Dec 2021 04:13:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (319 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:13:22: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:13:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:13:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:13:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569201/SRX10569201.20_summits.bed INFO @ Thu, 09 Dec 2021 04:13:37: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (143 records, 4 fields): 2 millis CompletedMACS2peakCalling