Job ID = 14160524 SRX = SRX8331159 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 38052982 spots for SRR11778472/SRR11778472.sra Written 38052982 spots for SRR11778472/SRR11778472.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160671 ("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: 00:11:58 38052982 reads; of these: 38052982 (100.00%) were unpaired; of these: 163292 (0.43%) aligned 0 times 32328540 (84.96%) aligned exactly 1 time 5561150 (14.61%) aligned >1 times 99.57% overall alignment rate Time searching: 00:11:58 Overall time: 00:11:58 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 16 files... [bam_rmdupse_core] 24440650 / 37889690 = 0.6450 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 03:18:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.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 03:18:30: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:18:30: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:18:35: 1000000 INFO @ Thu, 09 Dec 2021 03:18:40: 2000000 INFO @ Thu, 09 Dec 2021 03:18:46: 3000000 INFO @ Thu, 09 Dec 2021 03:18:51: 4000000 INFO @ Thu, 09 Dec 2021 03:18:56: 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 @ Thu, 09 Dec 2021 03:19:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.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 03:19:00: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:19:00: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:19:02: 6000000 INFO @ Thu, 09 Dec 2021 03:19:07: 1000000 INFO @ Thu, 09 Dec 2021 03:19:07: 7000000 INFO @ Thu, 09 Dec 2021 03:19:13: 8000000 INFO @ Thu, 09 Dec 2021 03:19:13: 2000000 INFO @ Thu, 09 Dec 2021 03:19:18: 9000000 INFO @ Thu, 09 Dec 2021 03:19:20: 3000000 INFO @ Thu, 09 Dec 2021 03:19:24: 10000000 INFO @ Thu, 09 Dec 2021 03:19:26: 4000000 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 03:19:30: 11000000 INFO @ Thu, 09 Dec 2021 03:19:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.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 03:19:30: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:19:30: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:19:33: 5000000 INFO @ Thu, 09 Dec 2021 03:19:35: 12000000 INFO @ Thu, 09 Dec 2021 03:19:36: 1000000 INFO @ Thu, 09 Dec 2021 03:19:39: 6000000 INFO @ Thu, 09 Dec 2021 03:19:41: 13000000 INFO @ Thu, 09 Dec 2021 03:19:41: 2000000 INFO @ Thu, 09 Dec 2021 03:19:43: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:19:43: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:19:43: #1 total tags in treatment: 13449040 INFO @ Thu, 09 Dec 2021 03:19:43: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:19:43: #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 03:19:44: #1 tags after filtering in treatment: 13449040 INFO @ Thu, 09 Dec 2021 03:19:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:19:44: #1 finished! INFO @ Thu, 09 Dec 2021 03:19:44: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:19:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:19:44: #2 number of paired peaks: 420 WARNING @ Thu, 09 Dec 2021 03:19:44: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Thu, 09 Dec 2021 03:19:44: start model_add_line... INFO @ Thu, 09 Dec 2021 03:19:45: start X-correlation... INFO @ Thu, 09 Dec 2021 03:19:45: end of X-cor INFO @ Thu, 09 Dec 2021 03:19:45: #2 finished! INFO @ Thu, 09 Dec 2021 03:19:45: #2 predicted fragment length is 68 bps INFO @ Thu, 09 Dec 2021 03:19:45: #2 alternative fragment length(s) may be 3,68 bps INFO @ Thu, 09 Dec 2021 03:19:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.05_model.r WARNING @ Thu, 09 Dec 2021 03:19:45: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:19:45: #2 You may need to consider one of the other alternative d(s): 3,68 WARNING @ Thu, 09 Dec 2021 03:19:45: #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 03:19:45: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:19:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:19:46: 7000000 INFO @ Thu, 09 Dec 2021 03:19:47: 3000000 INFO @ Thu, 09 Dec 2021 03:19:52: 8000000 INFO @ Thu, 09 Dec 2021 03:19:53: 4000000 INFO @ Thu, 09 Dec 2021 03:19:58: 5000000 INFO @ Thu, 09 Dec 2021 03:19:58: 9000000 INFO @ Thu, 09 Dec 2021 03:20:04: 6000000 INFO @ Thu, 09 Dec 2021 03:20:05: 10000000 INFO @ Thu, 09 Dec 2021 03:20:08: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:20:09: 7000000 INFO @ Thu, 09 Dec 2021 03:20:11: 11000000 INFO @ Thu, 09 Dec 2021 03:20:15: 8000000 INFO @ Thu, 09 Dec 2021 03:20:17: 12000000 INFO @ Thu, 09 Dec 2021 03:20:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:20:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:20:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.05_summits.bed INFO @ Thu, 09 Dec 2021 03:20:20: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (13880 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:20:20: 9000000 INFO @ Thu, 09 Dec 2021 03:20:24: 13000000 INFO @ Thu, 09 Dec 2021 03:20:26: 10000000 INFO @ Thu, 09 Dec 2021 03:20:26: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:20:26: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:20:26: #1 total tags in treatment: 13449040 INFO @ Thu, 09 Dec 2021 03:20:26: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:20:26: #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 03:20:27: #1 tags after filtering in treatment: 13449040 INFO @ Thu, 09 Dec 2021 03:20:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:20:27: #1 finished! INFO @ Thu, 09 Dec 2021 03:20:27: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:20:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:20:27: #2 number of paired peaks: 420 WARNING @ Thu, 09 Dec 2021 03:20:27: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Thu, 09 Dec 2021 03:20:27: start model_add_line... INFO @ Thu, 09 Dec 2021 03:20:28: start X-correlation... INFO @ Thu, 09 Dec 2021 03:20:28: end of X-cor INFO @ Thu, 09 Dec 2021 03:20:28: #2 finished! INFO @ Thu, 09 Dec 2021 03:20:28: #2 predicted fragment length is 68 bps INFO @ Thu, 09 Dec 2021 03:20:28: #2 alternative fragment length(s) may be 3,68 bps INFO @ Thu, 09 Dec 2021 03:20:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.10_model.r WARNING @ Thu, 09 Dec 2021 03:20:28: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:20:28: #2 You may need to consider one of the other alternative d(s): 3,68 WARNING @ Thu, 09 Dec 2021 03:20:28: #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 03:20:28: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:20:28: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:20:31: 11000000 INFO @ Thu, 09 Dec 2021 03:20:36: 12000000 INFO @ Thu, 09 Dec 2021 03:20:42: 13000000 INFO @ Thu, 09 Dec 2021 03:20:44: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:20:44: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:20:44: #1 total tags in treatment: 13449040 INFO @ Thu, 09 Dec 2021 03:20:44: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:20:44: #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 03:20:44: #1 tags after filtering in treatment: 13449040 INFO @ Thu, 09 Dec 2021 03:20:44: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:20:44: #1 finished! INFO @ Thu, 09 Dec 2021 03:20:44: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:20:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:20:45: #2 number of paired peaks: 420 WARNING @ Thu, 09 Dec 2021 03:20:45: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Thu, 09 Dec 2021 03:20:45: start model_add_line... INFO @ Thu, 09 Dec 2021 03:20:45: start X-correlation... INFO @ Thu, 09 Dec 2021 03:20:45: end of X-cor INFO @ Thu, 09 Dec 2021 03:20:45: #2 finished! INFO @ Thu, 09 Dec 2021 03:20:45: #2 predicted fragment length is 68 bps INFO @ Thu, 09 Dec 2021 03:20:45: #2 alternative fragment length(s) may be 3,68 bps INFO @ Thu, 09 Dec 2021 03:20:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.20_model.r WARNING @ Thu, 09 Dec 2021 03:20:45: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:20:45: #2 You may need to consider one of the other alternative d(s): 3,68 WARNING @ Thu, 09 Dec 2021 03:20:45: #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 03:20:45: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:20:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:20:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:21:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:21:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:21:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.10_summits.bed INFO @ Thu, 09 Dec 2021 03:21:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2291 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:21:08: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:21:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:21:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:21:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331159/SRX8331159.20_summits.bed INFO @ Thu, 09 Dec 2021 03:21:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (432 records, 4 fields): 11 millis CompletedMACS2peakCalling