Job ID = 14160620 SRX = SRX10399034 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 11279402 spots for SRR14022422/SRR14022422.sra Written 11279402 spots for SRR14022422/SRR14022422.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160740 ("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: 00:03:22 11279402 reads; of these: 11279402 (100.00%) were unpaired; of these: 1155391 (10.24%) aligned 0 times 8457963 (74.99%) aligned exactly 1 time 1666048 (14.77%) aligned >1 times 89.76% overall alignment rate Time searching: 00:03:22 Overall time: 00:03:22 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] 759005 / 10124011 = 0.0750 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 03:32:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.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 03:32:43: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:32:43: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:32:51: 1000000 INFO @ Thu, 09 Dec 2021 03:32:58: 2000000 INFO @ Thu, 09 Dec 2021 03:33:04: 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 03:33:10: 4000000 INFO @ Thu, 09 Dec 2021 03:33:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.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 03:33:13: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:33:13: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:33:17: 5000000 INFO @ Thu, 09 Dec 2021 03:33:19: 1000000 INFO @ Thu, 09 Dec 2021 03:33:25: 6000000 INFO @ Thu, 09 Dec 2021 03:33:26: 2000000 INFO @ Thu, 09 Dec 2021 03:33:31: 7000000 INFO @ Thu, 09 Dec 2021 03:33:33: 3000000 INFO @ Thu, 09 Dec 2021 03:33:37: 8000000 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 03:33:40: 4000000 INFO @ Thu, 09 Dec 2021 03:33:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.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 03:33:43: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:33:43: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:33:43: 9000000 INFO @ Thu, 09 Dec 2021 03:33:46: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:33:46: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:33:46: #1 total tags in treatment: 9365006 INFO @ Thu, 09 Dec 2021 03:33:46: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:33:46: #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 03:33:46: #1 tags after filtering in treatment: 9365006 INFO @ Thu, 09 Dec 2021 03:33:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:33:46: #1 finished! INFO @ Thu, 09 Dec 2021 03:33:46: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:33:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:33:47: #2 number of paired peaks: 312 WARNING @ Thu, 09 Dec 2021 03:33:47: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Thu, 09 Dec 2021 03:33:47: start model_add_line... INFO @ Thu, 09 Dec 2021 03:33:47: start X-correlation... INFO @ Thu, 09 Dec 2021 03:33:47: end of X-cor INFO @ Thu, 09 Dec 2021 03:33:47: #2 finished! INFO @ Thu, 09 Dec 2021 03:33:47: #2 predicted fragment length is 76 bps INFO @ Thu, 09 Dec 2021 03:33:47: #2 alternative fragment length(s) may be 4,76,584 bps INFO @ Thu, 09 Dec 2021 03:33:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.05_model.r WARNING @ Thu, 09 Dec 2021 03:33:47: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:33:47: #2 You may need to consider one of the other alternative d(s): 4,76,584 WARNING @ Thu, 09 Dec 2021 03:33:47: #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 03:33:47: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:33:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:33:49: 5000000 INFO @ Thu, 09 Dec 2021 03:33:51: 1000000 INFO @ Thu, 09 Dec 2021 03:33:57: 6000000 INFO @ Thu, 09 Dec 2021 03:33:58: 2000000 INFO @ Thu, 09 Dec 2021 03:34:05: 7000000 INFO @ Thu, 09 Dec 2021 03:34:06: 3000000 INFO @ Thu, 09 Dec 2021 03:34:08: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:34:12: 8000000 INFO @ Thu, 09 Dec 2021 03:34:13: 4000000 INFO @ Thu, 09 Dec 2021 03:34:19: 9000000 INFO @ Thu, 09 Dec 2021 03:34:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:34:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:34:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.05_summits.bed INFO @ Thu, 09 Dec 2021 03:34:20: Done! INFO @ Thu, 09 Dec 2021 03:34:20: 5000000 pass1 - making usageList (7 chroms): 23 millis pass2 - checking and writing primary data (529 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:34:21: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:34:21: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:34:21: #1 total tags in treatment: 9365006 INFO @ Thu, 09 Dec 2021 03:34:21: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:34:21: #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 03:34:21: #1 tags after filtering in treatment: 9365006 INFO @ Thu, 09 Dec 2021 03:34:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:34:21: #1 finished! INFO @ Thu, 09 Dec 2021 03:34:21: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:34:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:34:22: #2 number of paired peaks: 312 WARNING @ Thu, 09 Dec 2021 03:34:22: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Thu, 09 Dec 2021 03:34:22: start model_add_line... INFO @ Thu, 09 Dec 2021 03:34:22: start X-correlation... INFO @ Thu, 09 Dec 2021 03:34:22: end of X-cor INFO @ Thu, 09 Dec 2021 03:34:22: #2 finished! INFO @ Thu, 09 Dec 2021 03:34:22: #2 predicted fragment length is 76 bps INFO @ Thu, 09 Dec 2021 03:34:22: #2 alternative fragment length(s) may be 4,76,584 bps INFO @ Thu, 09 Dec 2021 03:34:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.10_model.r WARNING @ Thu, 09 Dec 2021 03:34:22: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:34:22: #2 You may need to consider one of the other alternative d(s): 4,76,584 WARNING @ Thu, 09 Dec 2021 03:34:22: #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 03:34:22: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:34:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:34:28: 6000000 INFO @ Thu, 09 Dec 2021 03:34:34: 7000000 INFO @ Thu, 09 Dec 2021 03:34:42: 8000000 INFO @ Thu, 09 Dec 2021 03:34:44: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:34:49: 9000000 INFO @ Thu, 09 Dec 2021 03:34:51: #1 tag size is determined as 76 bps INFO @ Thu, 09 Dec 2021 03:34:51: #1 tag size = 76 INFO @ Thu, 09 Dec 2021 03:34:51: #1 total tags in treatment: 9365006 INFO @ Thu, 09 Dec 2021 03:34:51: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:34:51: #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 03:34:51: #1 tags after filtering in treatment: 9365006 INFO @ Thu, 09 Dec 2021 03:34:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:34:51: #1 finished! INFO @ Thu, 09 Dec 2021 03:34:51: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:34:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:34:52: #2 number of paired peaks: 312 WARNING @ Thu, 09 Dec 2021 03:34:52: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Thu, 09 Dec 2021 03:34:52: start model_add_line... INFO @ Thu, 09 Dec 2021 03:34:52: start X-correlation... INFO @ Thu, 09 Dec 2021 03:34:52: end of X-cor INFO @ Thu, 09 Dec 2021 03:34:52: #2 finished! INFO @ Thu, 09 Dec 2021 03:34:52: #2 predicted fragment length is 76 bps INFO @ Thu, 09 Dec 2021 03:34:52: #2 alternative fragment length(s) may be 4,76,584 bps INFO @ Thu, 09 Dec 2021 03:34:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.20_model.r WARNING @ Thu, 09 Dec 2021 03:34:52: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:34:52: #2 You may need to consider one of the other alternative d(s): 4,76,584 WARNING @ Thu, 09 Dec 2021 03:34:52: #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 03:34:52: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:34:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:34:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:34:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:34:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.10_summits.bed INFO @ Thu, 09 Dec 2021 03:34:55: Done! pass1 - making usageList (7 chroms): 17 millis pass2 - checking and writing primary data (361 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:35:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:35:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:35:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:35:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10399034/SRX10399034.20_summits.bed INFO @ Thu, 09 Dec 2021 03:35:26: Done! pass1 - making usageList (6 chroms): 35 millis pass2 - checking and writing primary data (204 records, 4 fields): 24 millis CompletedMACS2peakCalling