Job ID = 14157858 SRX = SRX7879266 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 28254245 spots for SRR11272881/SRR11272881.sra Written 28254245 spots for SRR11272881/SRR11272881.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158013 ("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: 00:05:09 28254245 reads; of these: 28254245 (100.00%) were unpaired; of these: 5879421 (20.81%) aligned 0 times 18777576 (66.46%) aligned exactly 1 time 3597248 (12.73%) aligned >1 times 79.19% overall alignment rate Time searching: 00:05:09 Overall time: 00:05:09 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 12 files... [bam_rmdupse_core] 12522949 / 22374824 = 0.5597 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 @ Wed, 08 Dec 2021 11:52:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.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 @ Wed, 08 Dec 2021 11:52:11: #1 read tag files... INFO @ Wed, 08 Dec 2021 11:52:11: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 11:52:15: 1000000 INFO @ Wed, 08 Dec 2021 11:52:20: 2000000 INFO @ Wed, 08 Dec 2021 11:52:24: 3000000 INFO @ Wed, 08 Dec 2021 11:52:29: 4000000 INFO @ Wed, 08 Dec 2021 11:52:33: 5000000 INFO @ Wed, 08 Dec 2021 11:52:38: 6000000 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 @ Wed, 08 Dec 2021 11:52:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.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 @ Wed, 08 Dec 2021 11:52:41: #1 read tag files... INFO @ Wed, 08 Dec 2021 11:52:41: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 11:52:43: 7000000 INFO @ Wed, 08 Dec 2021 11:52:47: 1000000 INFO @ Wed, 08 Dec 2021 11:52:47: 8000000 INFO @ Wed, 08 Dec 2021 11:52:52: 9000000 INFO @ Wed, 08 Dec 2021 11:52:52: 2000000 INFO @ Wed, 08 Dec 2021 11:52:56: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 11:52:56: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 11:52:56: #1 total tags in treatment: 9851875 INFO @ Wed, 08 Dec 2021 11:52:56: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 11:52:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 11:52:56: #1 tags after filtering in treatment: 9851875 INFO @ Wed, 08 Dec 2021 11:52:56: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 11:52:56: #1 finished! INFO @ Wed, 08 Dec 2021 11:52:56: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 11:52:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 11:52:57: #2 number of paired peaks: 475 WARNING @ Wed, 08 Dec 2021 11:52:57: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Wed, 08 Dec 2021 11:52:57: start model_add_line... INFO @ Wed, 08 Dec 2021 11:52:57: start X-correlation... INFO @ Wed, 08 Dec 2021 11:52:57: end of X-cor INFO @ Wed, 08 Dec 2021 11:52:57: #2 finished! INFO @ Wed, 08 Dec 2021 11:52:57: #2 predicted fragment length is 44 bps INFO @ Wed, 08 Dec 2021 11:52:57: #2 alternative fragment length(s) may be 2,44,538 bps INFO @ Wed, 08 Dec 2021 11:52:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.05_model.r WARNING @ Wed, 08 Dec 2021 11:52:57: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 11:52:57: #2 You may need to consider one of the other alternative d(s): 2,44,538 WARNING @ Wed, 08 Dec 2021 11:52:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 11:52:57: #3 Call peaks... INFO @ Wed, 08 Dec 2021 11:52:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 11:52:58: 3000000 INFO @ Wed, 08 Dec 2021 11:53:03: 4000000 INFO @ Wed, 08 Dec 2021 11:53:09: 5000000 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 @ Wed, 08 Dec 2021 11:53:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.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 @ Wed, 08 Dec 2021 11:53:11: #1 read tag files... INFO @ Wed, 08 Dec 2021 11:53:11: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 11:53:14: 6000000 INFO @ Wed, 08 Dec 2021 11:53:15: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 11:53:16: 1000000 INFO @ Wed, 08 Dec 2021 11:53:19: 7000000 INFO @ Wed, 08 Dec 2021 11:53:21: 2000000 INFO @ Wed, 08 Dec 2021 11:53:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.05_peaks.xls INFO @ Wed, 08 Dec 2021 11:53:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 11:53:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.05_summits.bed INFO @ Wed, 08 Dec 2021 11:53:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (810 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 11:53:25: 8000000 INFO @ Wed, 08 Dec 2021 11:53:26: 3000000 INFO @ Wed, 08 Dec 2021 11:53:30: 9000000 INFO @ Wed, 08 Dec 2021 11:53:31: 4000000 INFO @ Wed, 08 Dec 2021 11:53:35: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 11:53:35: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 11:53:35: #1 total tags in treatment: 9851875 INFO @ Wed, 08 Dec 2021 11:53:35: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 11:53:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 11:53:35: #1 tags after filtering in treatment: 9851875 INFO @ Wed, 08 Dec 2021 11:53:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 11:53:35: #1 finished! INFO @ Wed, 08 Dec 2021 11:53:35: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 11:53:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 11:53:36: 5000000 INFO @ Wed, 08 Dec 2021 11:53:36: #2 number of paired peaks: 475 WARNING @ Wed, 08 Dec 2021 11:53:36: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Wed, 08 Dec 2021 11:53:36: start model_add_line... INFO @ Wed, 08 Dec 2021 11:53:36: start X-correlation... INFO @ Wed, 08 Dec 2021 11:53:36: end of X-cor INFO @ Wed, 08 Dec 2021 11:53:36: #2 finished! INFO @ Wed, 08 Dec 2021 11:53:36: #2 predicted fragment length is 44 bps INFO @ Wed, 08 Dec 2021 11:53:36: #2 alternative fragment length(s) may be 2,44,538 bps INFO @ Wed, 08 Dec 2021 11:53:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.10_model.r WARNING @ Wed, 08 Dec 2021 11:53:36: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 11:53:36: #2 You may need to consider one of the other alternative d(s): 2,44,538 WARNING @ Wed, 08 Dec 2021 11:53:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 11:53:36: #3 Call peaks... INFO @ Wed, 08 Dec 2021 11:53:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 11:53:40: 6000000 INFO @ Wed, 08 Dec 2021 11:53:45: 7000000 INFO @ Wed, 08 Dec 2021 11:53:50: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 11:53:54: 9000000 INFO @ Wed, 08 Dec 2021 11:53:55: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 11:53:58: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 11:53:58: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 11:53:58: #1 total tags in treatment: 9851875 INFO @ Wed, 08 Dec 2021 11:53:58: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 11:53:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 11:53:58: #1 tags after filtering in treatment: 9851875 INFO @ Wed, 08 Dec 2021 11:53:58: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 11:53:58: #1 finished! INFO @ Wed, 08 Dec 2021 11:53:58: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 11:53:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 11:53:59: #2 number of paired peaks: 475 WARNING @ Wed, 08 Dec 2021 11:53:59: Fewer paired peaks (475) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 475 pairs to build model! INFO @ Wed, 08 Dec 2021 11:53:59: start model_add_line... INFO @ Wed, 08 Dec 2021 11:53:59: start X-correlation... INFO @ Wed, 08 Dec 2021 11:53:59: end of X-cor INFO @ Wed, 08 Dec 2021 11:53:59: #2 finished! INFO @ Wed, 08 Dec 2021 11:53:59: #2 predicted fragment length is 44 bps INFO @ Wed, 08 Dec 2021 11:53:59: #2 alternative fragment length(s) may be 2,44,538 bps INFO @ Wed, 08 Dec 2021 11:53:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.20_model.r WARNING @ Wed, 08 Dec 2021 11:53:59: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 11:53:59: #2 You may need to consider one of the other alternative d(s): 2,44,538 WARNING @ Wed, 08 Dec 2021 11:53:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 11:53:59: #3 Call peaks... INFO @ Wed, 08 Dec 2021 11:53:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 11:54:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.10_peaks.xls INFO @ Wed, 08 Dec 2021 11:54:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 11:54:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.10_summits.bed INFO @ Wed, 08 Dec 2021 11:54:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (540 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 11:54:18: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 11:54:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.20_peaks.xls INFO @ Wed, 08 Dec 2021 11:54:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 11:54:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7879266/SRX7879266.20_summits.bed INFO @ Wed, 08 Dec 2021 11:54:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (205 records, 4 fields): 2 millis CompletedMACS2peakCalling