Job ID = 14157885 SRX = SRX10040016 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17069793 spots for SRR13642805/SRR13642805.sra Written 17069793 spots for SRR13642805/SRR13642805.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158078 ("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: 00:04:25 17069793 reads; of these: 17069793 (100.00%) were unpaired; of these: 192477 (1.13%) aligned 0 times 14337893 (84.00%) aligned exactly 1 time 2539423 (14.88%) aligned >1 times 98.87% overall alignment rate Time searching: 00:04:25 Overall time: 00:04:25 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] 2329203 / 16877316 = 0.1380 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 12:22:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.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 12:22:50: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:22:50: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:22:55: 1000000 INFO @ Wed, 08 Dec 2021 12:23:00: 2000000 INFO @ Wed, 08 Dec 2021 12:23:05: 3000000 INFO @ Wed, 08 Dec 2021 12:23:10: 4000000 INFO @ Wed, 08 Dec 2021 12:23:15: 5000000 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 12:23:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.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 12:23:19: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:23:19: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:23:20: 6000000 INFO @ Wed, 08 Dec 2021 12:23:25: 1000000 INFO @ Wed, 08 Dec 2021 12:23:26: 7000000 INFO @ Wed, 08 Dec 2021 12:23:31: 8000000 INFO @ Wed, 08 Dec 2021 12:23:31: 2000000 INFO @ Wed, 08 Dec 2021 12:23:36: 9000000 INFO @ Wed, 08 Dec 2021 12:23:37: 3000000 INFO @ Wed, 08 Dec 2021 12:23:41: 10000000 INFO @ Wed, 08 Dec 2021 12:23:43: 4000000 INFO @ Wed, 08 Dec 2021 12:23:47: 11000000 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 12:23:49: 5000000 INFO @ Wed, 08 Dec 2021 12:23:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.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 12:23:49: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:23:49: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:23:52: 12000000 INFO @ Wed, 08 Dec 2021 12:23:55: 6000000 INFO @ Wed, 08 Dec 2021 12:23:55: 1000000 INFO @ Wed, 08 Dec 2021 12:23:57: 13000000 INFO @ Wed, 08 Dec 2021 12:24:01: 7000000 INFO @ Wed, 08 Dec 2021 12:24:01: 2000000 INFO @ Wed, 08 Dec 2021 12:24:03: 14000000 INFO @ Wed, 08 Dec 2021 12:24:06: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:24:06: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:24:06: #1 total tags in treatment: 14548113 INFO @ Wed, 08 Dec 2021 12:24:06: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:24:06: #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 12:24:06: #1 tags after filtering in treatment: 14548113 INFO @ Wed, 08 Dec 2021 12:24:06: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:24:06: #1 finished! INFO @ Wed, 08 Dec 2021 12:24:06: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:24:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:24:06: 8000000 INFO @ Wed, 08 Dec 2021 12:24:07: #2 number of paired peaks: 111 WARNING @ Wed, 08 Dec 2021 12:24:07: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Wed, 08 Dec 2021 12:24:07: start model_add_line... INFO @ Wed, 08 Dec 2021 12:24:07: start X-correlation... INFO @ Wed, 08 Dec 2021 12:24:07: end of X-cor INFO @ Wed, 08 Dec 2021 12:24:07: #2 finished! INFO @ Wed, 08 Dec 2021 12:24:07: #2 predicted fragment length is 54 bps INFO @ Wed, 08 Dec 2021 12:24:07: #2 alternative fragment length(s) may be 1,36,54,384,406,484,524,571 bps INFO @ Wed, 08 Dec 2021 12:24:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.05_model.r WARNING @ Wed, 08 Dec 2021 12:24:07: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:24:07: #2 You may need to consider one of the other alternative d(s): 1,36,54,384,406,484,524,571 WARNING @ Wed, 08 Dec 2021 12:24:07: #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 12:24:07: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:24:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:24:07: 3000000 INFO @ Wed, 08 Dec 2021 12:24:12: 9000000 INFO @ Wed, 08 Dec 2021 12:24:13: 4000000 INFO @ Wed, 08 Dec 2021 12:24:18: 10000000 INFO @ Wed, 08 Dec 2021 12:24:20: 5000000 INFO @ Wed, 08 Dec 2021 12:24:24: 11000000 INFO @ Wed, 08 Dec 2021 12:24:26: 6000000 INFO @ Wed, 08 Dec 2021 12:24:30: 12000000 INFO @ Wed, 08 Dec 2021 12:24:32: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:24:33: 7000000 INFO @ Wed, 08 Dec 2021 12:24:36: 13000000 INFO @ Wed, 08 Dec 2021 12:24:39: 8000000 INFO @ Wed, 08 Dec 2021 12:24:41: 14000000 INFO @ Wed, 08 Dec 2021 12:24:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.05_peaks.xls INFO @ Wed, 08 Dec 2021 12:24:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:24:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.05_summits.bed INFO @ Wed, 08 Dec 2021 12:24:43: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (542 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:24:45: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:24:45: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:24:45: #1 total tags in treatment: 14548113 INFO @ Wed, 08 Dec 2021 12:24:45: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:24:45: #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 12:24:45: #1 tags after filtering in treatment: 14548113 INFO @ Wed, 08 Dec 2021 12:24:45: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:24:45: #1 finished! INFO @ Wed, 08 Dec 2021 12:24:45: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:24:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:24:45: 9000000 INFO @ Wed, 08 Dec 2021 12:24:46: #2 number of paired peaks: 111 WARNING @ Wed, 08 Dec 2021 12:24:46: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Wed, 08 Dec 2021 12:24:46: start model_add_line... INFO @ Wed, 08 Dec 2021 12:24:46: start X-correlation... INFO @ Wed, 08 Dec 2021 12:24:46: end of X-cor INFO @ Wed, 08 Dec 2021 12:24:46: #2 finished! INFO @ Wed, 08 Dec 2021 12:24:46: #2 predicted fragment length is 54 bps INFO @ Wed, 08 Dec 2021 12:24:46: #2 alternative fragment length(s) may be 1,36,54,384,406,484,524,571 bps INFO @ Wed, 08 Dec 2021 12:24:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.10_model.r WARNING @ Wed, 08 Dec 2021 12:24:46: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:24:46: #2 You may need to consider one of the other alternative d(s): 1,36,54,384,406,484,524,571 WARNING @ Wed, 08 Dec 2021 12:24:46: #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 12:24:46: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:24:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:24:52: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 12:24:58: 11000000 INFO @ Wed, 08 Dec 2021 12:25:03: 12000000 INFO @ Wed, 08 Dec 2021 12:25:09: 13000000 INFO @ Wed, 08 Dec 2021 12:25:11: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:25:15: 14000000 INFO @ Wed, 08 Dec 2021 12:25:18: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 12:25:18: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 12:25:18: #1 total tags in treatment: 14548113 INFO @ Wed, 08 Dec 2021 12:25:18: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:25:18: #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 12:25:19: #1 tags after filtering in treatment: 14548113 INFO @ Wed, 08 Dec 2021 12:25:19: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:25:19: #1 finished! INFO @ Wed, 08 Dec 2021 12:25:19: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:25:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:25:20: #2 number of paired peaks: 111 WARNING @ Wed, 08 Dec 2021 12:25:20: Fewer paired peaks (111) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 111 pairs to build model! INFO @ Wed, 08 Dec 2021 12:25:20: start model_add_line... INFO @ Wed, 08 Dec 2021 12:25:20: start X-correlation... INFO @ Wed, 08 Dec 2021 12:25:20: end of X-cor INFO @ Wed, 08 Dec 2021 12:25:20: #2 finished! INFO @ Wed, 08 Dec 2021 12:25:20: #2 predicted fragment length is 54 bps INFO @ Wed, 08 Dec 2021 12:25:20: #2 alternative fragment length(s) may be 1,36,54,384,406,484,524,571 bps INFO @ Wed, 08 Dec 2021 12:25:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.20_model.r WARNING @ Wed, 08 Dec 2021 12:25:20: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:25:20: #2 You may need to consider one of the other alternative d(s): 1,36,54,384,406,484,524,571 WARNING @ Wed, 08 Dec 2021 12:25:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 12:25:20: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:25:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:25:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.10_peaks.xls INFO @ Wed, 08 Dec 2021 12:25:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:25:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.10_summits.bed INFO @ Wed, 08 Dec 2021 12:25:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (289 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 12:25:45: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:25:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.20_peaks.xls INFO @ Wed, 08 Dec 2021 12:25:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:25:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10040016/SRX10040016.20_summits.bed INFO @ Wed, 08 Dec 2021 12:25:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (83 records, 4 fields): 1 millis CompletedMACS2peakCalling