Job ID = 14157879 SRX = SRX10040010 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17754014 spots for SRR13642811/SRR13642811.sra Written 17754014 spots for SRR13642811/SRR13642811.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158075 ("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: 00:04:36 17754014 reads; of these: 17754014 (100.00%) were unpaired; of these: 406167 (2.29%) aligned 0 times 14871321 (83.76%) aligned exactly 1 time 2476526 (13.95%) aligned >1 times 97.71% overall alignment rate Time searching: 00:04:36 Overall time: 00:04:36 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] 2364699 / 17347847 = 0.1363 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 12:21:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.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 12:21:28: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:21:28: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:21:34: 1000000 INFO @ Wed, 08 Dec 2021 12:21:40: 2000000 INFO @ Wed, 08 Dec 2021 12:21:46: 3000000 INFO @ Wed, 08 Dec 2021 12:21:51: 4000000 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 12:21:57: 5000000 INFO @ Wed, 08 Dec 2021 12:21:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.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 12:21:58: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:21:58: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:22:03: 6000000 INFO @ Wed, 08 Dec 2021 12:22:03: 1000000 INFO @ Wed, 08 Dec 2021 12:22:08: 2000000 INFO @ Wed, 08 Dec 2021 12:22:08: 7000000 INFO @ Wed, 08 Dec 2021 12:22:14: 3000000 INFO @ Wed, 08 Dec 2021 12:22:14: 8000000 INFO @ Wed, 08 Dec 2021 12:22:19: 4000000 INFO @ Wed, 08 Dec 2021 12:22:20: 9000000 INFO @ Wed, 08 Dec 2021 12:22:24: 5000000 INFO @ Wed, 08 Dec 2021 12:22:26: 10000000 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 12:22:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.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 12:22:28: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:22:28: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:22:29: 6000000 INFO @ Wed, 08 Dec 2021 12:22:32: 11000000 INFO @ Wed, 08 Dec 2021 12:22:34: 7000000 INFO @ Wed, 08 Dec 2021 12:22:34: 1000000 INFO @ Wed, 08 Dec 2021 12:22:37: 12000000 INFO @ Wed, 08 Dec 2021 12:22:39: 8000000 INFO @ Wed, 08 Dec 2021 12:22:40: 2000000 INFO @ Wed, 08 Dec 2021 12:22:43: 13000000 INFO @ Wed, 08 Dec 2021 12:22:44: 9000000 INFO @ Wed, 08 Dec 2021 12:22:45: 3000000 INFO @ Wed, 08 Dec 2021 12:22:49: 14000000 INFO @ Wed, 08 Dec 2021 12:22:49: 10000000 INFO @ Wed, 08 Dec 2021 12:22:50: 4000000 INFO @ Wed, 08 Dec 2021 12:22:54: 11000000 INFO @ Wed, 08 Dec 2021 12:22:55: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:22:55: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:22:55: #1 total tags in treatment: 14983148 INFO @ Wed, 08 Dec 2021 12:22:55: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:22:55: #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 12:22:55: #1 tags after filtering in treatment: 14983148 INFO @ Wed, 08 Dec 2021 12:22:55: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:22:55: #1 finished! INFO @ Wed, 08 Dec 2021 12:22:55: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:22:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:22:56: 5000000 INFO @ Wed, 08 Dec 2021 12:22:56: #2 number of paired peaks: 107 WARNING @ Wed, 08 Dec 2021 12:22:56: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Wed, 08 Dec 2021 12:22:56: start model_add_line... INFO @ Wed, 08 Dec 2021 12:22:56: start X-correlation... INFO @ Wed, 08 Dec 2021 12:22:56: end of X-cor INFO @ Wed, 08 Dec 2021 12:22:56: #2 finished! INFO @ Wed, 08 Dec 2021 12:22:56: #2 predicted fragment length is 52 bps INFO @ Wed, 08 Dec 2021 12:22:56: #2 alternative fragment length(s) may be 1,52,189,492,539 bps INFO @ Wed, 08 Dec 2021 12:22:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.05_model.r WARNING @ Wed, 08 Dec 2021 12:22:56: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:22:56: #2 You may need to consider one of the other alternative d(s): 1,52,189,492,539 WARNING @ Wed, 08 Dec 2021 12:22:56: #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 12:22:56: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:22:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:22:59: 12000000 INFO @ Wed, 08 Dec 2021 12:23:01: 6000000 INFO @ Wed, 08 Dec 2021 12:23:04: 13000000 INFO @ Wed, 08 Dec 2021 12:23:06: 7000000 INFO @ Wed, 08 Dec 2021 12:23:09: 14000000 INFO @ Wed, 08 Dec 2021 12:23:11: 8000000 INFO @ Wed, 08 Dec 2021 12:23:14: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:23:14: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:23:14: #1 total tags in treatment: 14983148 INFO @ Wed, 08 Dec 2021 12:23:14: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:23:14: #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 12:23:14: #1 tags after filtering in treatment: 14983148 INFO @ Wed, 08 Dec 2021 12:23:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:23:14: #1 finished! INFO @ Wed, 08 Dec 2021 12:23:14: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:23:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:23:15: #2 number of paired peaks: 107 WARNING @ Wed, 08 Dec 2021 12:23:15: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Wed, 08 Dec 2021 12:23:15: start model_add_line... INFO @ Wed, 08 Dec 2021 12:23:15: start X-correlation... INFO @ Wed, 08 Dec 2021 12:23:16: end of X-cor INFO @ Wed, 08 Dec 2021 12:23:16: #2 finished! INFO @ Wed, 08 Dec 2021 12:23:16: #2 predicted fragment length is 52 bps INFO @ Wed, 08 Dec 2021 12:23:16: #2 alternative fragment length(s) may be 1,52,189,492,539 bps INFO @ Wed, 08 Dec 2021 12:23:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.10_model.r WARNING @ Wed, 08 Dec 2021 12:23:16: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:23:16: #2 You may need to consider one of the other alternative d(s): 1,52,189,492,539 WARNING @ Wed, 08 Dec 2021 12:23:16: #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 12:23:16: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:23:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:23:16: 9000000 INFO @ Wed, 08 Dec 2021 12:23:21: 10000000 INFO @ Wed, 08 Dec 2021 12:23:22: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:23:26: 11000000 INFO @ Wed, 08 Dec 2021 12:23:31: 12000000 INFO @ Wed, 08 Dec 2021 12:23:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.05_peaks.xls INFO @ Wed, 08 Dec 2021 12:23:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:23:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.05_summits.bed INFO @ Wed, 08 Dec 2021 12:23:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (572 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:23:36: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 12:23:41: 14000000 INFO @ Wed, 08 Dec 2021 12:23:42: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:23:46: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:23:46: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:23:46: #1 total tags in treatment: 14983148 INFO @ Wed, 08 Dec 2021 12:23:46: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:23:46: #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 12:23:46: #1 tags after filtering in treatment: 14983148 INFO @ Wed, 08 Dec 2021 12:23:46: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:23:46: #1 finished! INFO @ Wed, 08 Dec 2021 12:23:46: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:23:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:23:47: #2 number of paired peaks: 107 WARNING @ Wed, 08 Dec 2021 12:23:47: Fewer paired peaks (107) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 107 pairs to build model! INFO @ Wed, 08 Dec 2021 12:23:47: start model_add_line... INFO @ Wed, 08 Dec 2021 12:23:47: start X-correlation... INFO @ Wed, 08 Dec 2021 12:23:47: end of X-cor INFO @ Wed, 08 Dec 2021 12:23:47: #2 finished! INFO @ Wed, 08 Dec 2021 12:23:47: #2 predicted fragment length is 52 bps INFO @ Wed, 08 Dec 2021 12:23:47: #2 alternative fragment length(s) may be 1,52,189,492,539 bps INFO @ Wed, 08 Dec 2021 12:23:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.20_model.r WARNING @ Wed, 08 Dec 2021 12:23:47: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:23:47: #2 You may need to consider one of the other alternative d(s): 1,52,189,492,539 WARNING @ Wed, 08 Dec 2021 12:23:47: #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 12:23:47: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:23:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:23:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.10_peaks.xls INFO @ Wed, 08 Dec 2021 12:23:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:23:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.10_summits.bed INFO @ Wed, 08 Dec 2021 12:23:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (301 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:24:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 12:24:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.20_peaks.xls INFO @ Wed, 08 Dec 2021 12:24:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:24:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10040010/SRX10040010.20_summits.bed INFO @ Wed, 08 Dec 2021 12:24:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (96 records, 4 fields): 1 millis CompletedMACS2peakCalling