Job ID = 14159671 SRX = SRX3180790 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 13244524 spots for SRR6030441/SRR6030441.sra Written 13244524 spots for SRR6030441/SRR6030441.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160283 ("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: 00:04:55 13244524 reads; of these: 13244524 (100.00%) were unpaired; of these: 343393 (2.59%) aligned 0 times 10558686 (79.72%) aligned exactly 1 time 2342445 (17.69%) aligned >1 times 97.41% overall alignment rate Time searching: 00:04:55 Overall time: 00:04:55 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] 1468500 / 12901131 = 0.1138 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 00:22:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.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 00:22:33: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:22:33: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:22:41: 1000000 INFO @ Thu, 09 Dec 2021 00:22:49: 2000000 INFO @ Thu, 09 Dec 2021 00:22:56: 3000000 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 00:23:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.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 00:23:01: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:23:01: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:23:04: 4000000 INFO @ Thu, 09 Dec 2021 00:23:11: 5000000 INFO @ Thu, 09 Dec 2021 00:23:12: 1000000 INFO @ Thu, 09 Dec 2021 00:23:19: 6000000 INFO @ Thu, 09 Dec 2021 00:23:21: 2000000 INFO @ Thu, 09 Dec 2021 00:23:26: 7000000 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 00:23:30: 3000000 INFO @ Thu, 09 Dec 2021 00:23:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.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 00:23:31: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:23:31: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:23:34: 8000000 INFO @ Thu, 09 Dec 2021 00:23:40: 4000000 INFO @ Thu, 09 Dec 2021 00:23:41: 9000000 INFO @ Thu, 09 Dec 2021 00:23:42: 1000000 INFO @ Thu, 09 Dec 2021 00:23:49: 10000000 INFO @ Thu, 09 Dec 2021 00:23:49: 5000000 INFO @ Thu, 09 Dec 2021 00:23:52: 2000000 INFO @ Thu, 09 Dec 2021 00:23:56: 11000000 INFO @ Thu, 09 Dec 2021 00:23:59: 6000000 INFO @ Thu, 09 Dec 2021 00:24:00: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 00:24:00: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 00:24:00: #1 total tags in treatment: 11432631 INFO @ Thu, 09 Dec 2021 00:24:00: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:24:00: #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 00:24:00: #1 tags after filtering in treatment: 11432631 INFO @ Thu, 09 Dec 2021 00:24:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:24:00: #1 finished! INFO @ Thu, 09 Dec 2021 00:24:00: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:24:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:24:01: 3000000 INFO @ Thu, 09 Dec 2021 00:24:01: #2 number of paired peaks: 401 WARNING @ Thu, 09 Dec 2021 00:24:01: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Thu, 09 Dec 2021 00:24:01: start model_add_line... INFO @ Thu, 09 Dec 2021 00:24:01: start X-correlation... INFO @ Thu, 09 Dec 2021 00:24:01: end of X-cor INFO @ Thu, 09 Dec 2021 00:24:01: #2 finished! INFO @ Thu, 09 Dec 2021 00:24:01: #2 predicted fragment length is 48 bps INFO @ Thu, 09 Dec 2021 00:24:01: #2 alternative fragment length(s) may be 2,48,553 bps INFO @ Thu, 09 Dec 2021 00:24:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.05_model.r WARNING @ Thu, 09 Dec 2021 00:24:01: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:24:01: #2 You may need to consider one of the other alternative d(s): 2,48,553 WARNING @ Thu, 09 Dec 2021 00:24:01: #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 00:24:01: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:24:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:24:08: 7000000 INFO @ Thu, 09 Dec 2021 00:24:10: 4000000 INFO @ Thu, 09 Dec 2021 00:24:17: 8000000 INFO @ Thu, 09 Dec 2021 00:24:20: 5000000 INFO @ Thu, 09 Dec 2021 00:24:27: 9000000 INFO @ Thu, 09 Dec 2021 00:24:28: 6000000 INFO @ Thu, 09 Dec 2021 00:24:32: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:24:35: 10000000 INFO @ Thu, 09 Dec 2021 00:24:38: 7000000 INFO @ Thu, 09 Dec 2021 00:24:44: 11000000 INFO @ Thu, 09 Dec 2021 00:24:47: 8000000 INFO @ Thu, 09 Dec 2021 00:24:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:24:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:24:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.05_summits.bed INFO @ Thu, 09 Dec 2021 00:24:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (684 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:24:48: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 00:24:48: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 00:24:48: #1 total tags in treatment: 11432631 INFO @ Thu, 09 Dec 2021 00:24:48: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:24:48: #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 00:24:48: #1 tags after filtering in treatment: 11432631 INFO @ Thu, 09 Dec 2021 00:24:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:24:48: #1 finished! INFO @ Thu, 09 Dec 2021 00:24:48: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:24:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:24:49: #2 number of paired peaks: 401 WARNING @ Thu, 09 Dec 2021 00:24:49: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Thu, 09 Dec 2021 00:24:49: start model_add_line... INFO @ Thu, 09 Dec 2021 00:24:49: start X-correlation... INFO @ Thu, 09 Dec 2021 00:24:49: end of X-cor INFO @ Thu, 09 Dec 2021 00:24:49: #2 finished! INFO @ Thu, 09 Dec 2021 00:24:49: #2 predicted fragment length is 48 bps INFO @ Thu, 09 Dec 2021 00:24:49: #2 alternative fragment length(s) may be 2,48,553 bps INFO @ Thu, 09 Dec 2021 00:24:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.10_model.r WARNING @ Thu, 09 Dec 2021 00:24:49: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:24:49: #2 You may need to consider one of the other alternative d(s): 2,48,553 WARNING @ Thu, 09 Dec 2021 00:24:49: #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 00:24:49: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:24:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:24:56: 9000000 INFO @ Thu, 09 Dec 2021 00:25:05: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:25:14: 11000000 INFO @ Thu, 09 Dec 2021 00:25:19: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 00:25:19: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 00:25:19: #1 total tags in treatment: 11432631 INFO @ Thu, 09 Dec 2021 00:25:19: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:25:19: #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 00:25:19: #1 tags after filtering in treatment: 11432631 INFO @ Thu, 09 Dec 2021 00:25:19: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:25:19: #1 finished! INFO @ Thu, 09 Dec 2021 00:25:19: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:25:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:25:20: #2 number of paired peaks: 401 WARNING @ Thu, 09 Dec 2021 00:25:20: Fewer paired peaks (401) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 401 pairs to build model! INFO @ Thu, 09 Dec 2021 00:25:20: start model_add_line... INFO @ Thu, 09 Dec 2021 00:25:20: start X-correlation... INFO @ Thu, 09 Dec 2021 00:25:20: end of X-cor INFO @ Thu, 09 Dec 2021 00:25:20: #2 finished! INFO @ Thu, 09 Dec 2021 00:25:20: #2 predicted fragment length is 48 bps INFO @ Thu, 09 Dec 2021 00:25:20: #2 alternative fragment length(s) may be 2,48,553 bps INFO @ Thu, 09 Dec 2021 00:25:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.20_model.r WARNING @ Thu, 09 Dec 2021 00:25:20: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:25:20: #2 You may need to consider one of the other alternative d(s): 2,48,553 WARNING @ Thu, 09 Dec 2021 00:25:20: #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 00:25:20: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:25:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:25:23: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:25:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:25:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:25:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.10_summits.bed INFO @ Thu, 09 Dec 2021 00:25:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (430 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:25:53: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:26:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:26:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:26:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX3180790/SRX3180790.20_summits.bed INFO @ Thu, 09 Dec 2021 00:26:08: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (193 records, 4 fields): 2 millis CompletedMACS2peakCalling