Job ID = 14160718 SRX = SRX10569205 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2021-12-08T18:52:31 prefetch.2.10.7: 1) Downloading 'SRR14202287'... 2021-12-08T18:52:31 prefetch.2.10.7: Downloading via HTTPS... 2021-12-08T18:54:03 prefetch.2.10.7: HTTPS download succeed 2021-12-08T18:54:03 prefetch.2.10.7: 1) 'SRR14202287' was downloaded successfully 2021-12-08T18:54:03 prefetch.2.10.7: 'SRR14202287' has 0 unresolved dependencies Read 20327392 spots for SRR14202287/SRR14202287.sra Written 20327392 spots for SRR14202287/SRR14202287.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160868 ("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: 00:11:05 20327392 reads; of these: 20327392 (100.00%) were unpaired; of these: 8214622 (40.41%) aligned 0 times 8504095 (41.84%) aligned exactly 1 time 3608675 (17.75%) aligned >1 times 59.59% overall alignment rate Time searching: 00:11:05 Overall time: 00:11:05 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] 2633049 / 12112770 = 0.2174 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 04:12:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.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 04:12:26: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:12:26: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:12:39: 1000000 INFO @ Thu, 09 Dec 2021 04:12:51: 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 04:12:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.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 04:12:56: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:12:56: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:13:06: 3000000 INFO @ Thu, 09 Dec 2021 04:13:09: 1000000 INFO @ Thu, 09 Dec 2021 04:13:20: 4000000 INFO @ Thu, 09 Dec 2021 04:13:22: 2000000 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 04:13:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.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 04:13:26: #1 read tag files... INFO @ Thu, 09 Dec 2021 04:13:26: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 04:13:34: 5000000 INFO @ Thu, 09 Dec 2021 04:13:35: 3000000 INFO @ Thu, 09 Dec 2021 04:13:41: 1000000 INFO @ Thu, 09 Dec 2021 04:13:48: 4000000 INFO @ Thu, 09 Dec 2021 04:13:50: 6000000 INFO @ Thu, 09 Dec 2021 04:13:56: 2000000 INFO @ Thu, 09 Dec 2021 04:14:01: 5000000 INFO @ Thu, 09 Dec 2021 04:14:05: 7000000 INFO @ Thu, 09 Dec 2021 04:14:10: 3000000 INFO @ Thu, 09 Dec 2021 04:14:13: 6000000 INFO @ Thu, 09 Dec 2021 04:14:20: 8000000 INFO @ Thu, 09 Dec 2021 04:14:24: 4000000 INFO @ Thu, 09 Dec 2021 04:14:26: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 04:14:35: 9000000 INFO @ Thu, 09 Dec 2021 04:14:39: 8000000 INFO @ Thu, 09 Dec 2021 04:14:39: 5000000 INFO @ Thu, 09 Dec 2021 04:14:42: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:14:42: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:14:42: #1 total tags in treatment: 9479721 INFO @ Thu, 09 Dec 2021 04:14:42: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:14:42: #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 04:14:42: #1 tags after filtering in treatment: 9479721 INFO @ Thu, 09 Dec 2021 04:14:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:14:42: #1 finished! INFO @ Thu, 09 Dec 2021 04:14:42: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:14:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:14:43: #2 number of paired peaks: 414 WARNING @ Thu, 09 Dec 2021 04:14:43: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Thu, 09 Dec 2021 04:14:43: start model_add_line... INFO @ Thu, 09 Dec 2021 04:14:43: start X-correlation... INFO @ Thu, 09 Dec 2021 04:14:43: end of X-cor INFO @ Thu, 09 Dec 2021 04:14:43: #2 finished! INFO @ Thu, 09 Dec 2021 04:14:43: #2 predicted fragment length is 60 bps INFO @ Thu, 09 Dec 2021 04:14:43: #2 alternative fragment length(s) may be 3,60,558 bps INFO @ Thu, 09 Dec 2021 04:14:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.05_model.r WARNING @ Thu, 09 Dec 2021 04:14:43: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:14:43: #2 You may need to consider one of the other alternative d(s): 3,60,558 WARNING @ Thu, 09 Dec 2021 04:14:43: #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 04:14:43: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:14:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:14:51: 9000000 INFO @ Thu, 09 Dec 2021 04:14:52: 6000000 INFO @ Thu, 09 Dec 2021 04:14:57: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:14:57: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:14:57: #1 total tags in treatment: 9479721 INFO @ Thu, 09 Dec 2021 04:14:57: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:14:57: #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 04:14:57: #1 tags after filtering in treatment: 9479721 INFO @ Thu, 09 Dec 2021 04:14:57: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:14:57: #1 finished! INFO @ Thu, 09 Dec 2021 04:14:57: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:14:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:14:58: #2 number of paired peaks: 414 WARNING @ Thu, 09 Dec 2021 04:14:58: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Thu, 09 Dec 2021 04:14:58: start model_add_line... INFO @ Thu, 09 Dec 2021 04:14:58: start X-correlation... INFO @ Thu, 09 Dec 2021 04:14:58: end of X-cor INFO @ Thu, 09 Dec 2021 04:14:58: #2 finished! INFO @ Thu, 09 Dec 2021 04:14:58: #2 predicted fragment length is 60 bps INFO @ Thu, 09 Dec 2021 04:14:58: #2 alternative fragment length(s) may be 3,60,558 bps INFO @ Thu, 09 Dec 2021 04:14:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.10_model.r WARNING @ Thu, 09 Dec 2021 04:14:58: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:14:58: #2 You may need to consider one of the other alternative d(s): 3,60,558 WARNING @ Thu, 09 Dec 2021 04:14:58: #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 04:14:58: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:14:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 04:15:05: 7000000 INFO @ Thu, 09 Dec 2021 04:15:10: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:15:17: 8000000 INFO @ Thu, 09 Dec 2021 04:15:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.05_peaks.xls INFO @ Thu, 09 Dec 2021 04:15:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:15:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.05_summits.bed INFO @ Thu, 09 Dec 2021 04:15:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (636 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:15:24: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:15:29: 9000000 INFO @ Thu, 09 Dec 2021 04:15:35: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 04:15:35: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 04:15:35: #1 total tags in treatment: 9479721 INFO @ Thu, 09 Dec 2021 04:15:35: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 04:15:35: #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 04:15:36: #1 tags after filtering in treatment: 9479721 INFO @ Thu, 09 Dec 2021 04:15:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 04:15:36: #1 finished! INFO @ Thu, 09 Dec 2021 04:15:36: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 04:15:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 04:15:37: #2 number of paired peaks: 414 WARNING @ Thu, 09 Dec 2021 04:15:37: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Thu, 09 Dec 2021 04:15:37: start model_add_line... INFO @ Thu, 09 Dec 2021 04:15:37: start X-correlation... INFO @ Thu, 09 Dec 2021 04:15:37: end of X-cor INFO @ Thu, 09 Dec 2021 04:15:37: #2 finished! INFO @ Thu, 09 Dec 2021 04:15:37: #2 predicted fragment length is 60 bps INFO @ Thu, 09 Dec 2021 04:15:37: #2 alternative fragment length(s) may be 3,60,558 bps INFO @ Thu, 09 Dec 2021 04:15:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.20_model.r WARNING @ Thu, 09 Dec 2021 04:15:37: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 04:15:37: #2 You may need to consider one of the other alternative d(s): 3,60,558 WARNING @ Thu, 09 Dec 2021 04:15:37: #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 04:15:37: #3 Call peaks... INFO @ Thu, 09 Dec 2021 04:15:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 04:15:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.10_peaks.xls INFO @ Thu, 09 Dec 2021 04:15:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:15:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.10_summits.bed INFO @ Thu, 09 Dec 2021 04:15:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (458 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 04:16:03: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 04:16:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.20_peaks.xls INFO @ Thu, 09 Dec 2021 04:16:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 04:16:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569205/SRX10569205.20_summits.bed INFO @ Thu, 09 Dec 2021 04:16:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (218 records, 4 fields): 2 millis CompletedMACS2peakCalling