Job ID = 12264795 SRX = SRX4082401 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 114856380 spots for SRR7164238/SRR7164238.sra Written 114856380 spots for SRR7164238/SRR7164238.sra Read 101998631 spots for SRR7164239/SRR7164239.sra Written 101998631 spots for SRR7164239/SRR7164239.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265426 ("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: 00:24:21 216855011 reads; of these: 216855011 (100.00%) were unpaired; of these: 152786588 (70.46%) aligned 0 times 56464771 (26.04%) aligned exactly 1 time 7603652 (3.51%) aligned >1 times 29.54% overall alignment rate Time searching: 00:24:21 Overall time: 00:24:21 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 28 files... [bam_rmdupse_core] 43013757 / 64068423 = 0.6714 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:47:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.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 @ Sat, 03 Apr 2021 06:47:32: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:47:32: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:47:38: 1000000 INFO @ Sat, 03 Apr 2021 06:47:44: 2000000 INFO @ Sat, 03 Apr 2021 06:47:50: 3000000 INFO @ Sat, 03 Apr 2021 06:47:56: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:48:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.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 @ Sat, 03 Apr 2021 06:48:00: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:48:00: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:48:02: 5000000 INFO @ Sat, 03 Apr 2021 06:48:07: 1000000 INFO @ Sat, 03 Apr 2021 06:48:10: 6000000 INFO @ Sat, 03 Apr 2021 06:48:15: 2000000 INFO @ Sat, 03 Apr 2021 06:48:17: 7000000 INFO @ Sat, 03 Apr 2021 06:48:22: 3000000 INFO @ Sat, 03 Apr 2021 06:48:23: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:48:28: 4000000 INFO @ Sat, 03 Apr 2021 06:48:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.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 @ Sat, 03 Apr 2021 06:48:31: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:48:31: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:48:31: 9000000 INFO @ Sat, 03 Apr 2021 06:48:34: 5000000 INFO @ Sat, 03 Apr 2021 06:48:38: 10000000 INFO @ Sat, 03 Apr 2021 06:48:39: 1000000 INFO @ Sat, 03 Apr 2021 06:48:41: 6000000 INFO @ Sat, 03 Apr 2021 06:48:46: 11000000 INFO @ Sat, 03 Apr 2021 06:48:46: 2000000 INFO @ Sat, 03 Apr 2021 06:48:48: 7000000 INFO @ Sat, 03 Apr 2021 06:48:52: 12000000 INFO @ Sat, 03 Apr 2021 06:48:54: 3000000 INFO @ Sat, 03 Apr 2021 06:48:56: 8000000 INFO @ Sat, 03 Apr 2021 06:48:59: 13000000 INFO @ Sat, 03 Apr 2021 06:49:01: 4000000 INFO @ Sat, 03 Apr 2021 06:49:03: 9000000 INFO @ Sat, 03 Apr 2021 06:49:05: 14000000 INFO @ Sat, 03 Apr 2021 06:49:09: 5000000 INFO @ Sat, 03 Apr 2021 06:49:10: 10000000 INFO @ Sat, 03 Apr 2021 06:49:12: 15000000 INFO @ Sat, 03 Apr 2021 06:49:17: 6000000 INFO @ Sat, 03 Apr 2021 06:49:18: 16000000 INFO @ Sat, 03 Apr 2021 06:49:18: 11000000 INFO @ Sat, 03 Apr 2021 06:49:24: 7000000 INFO @ Sat, 03 Apr 2021 06:49:26: 17000000 INFO @ Sat, 03 Apr 2021 06:49:26: 12000000 INFO @ Sat, 03 Apr 2021 06:49:32: 18000000 INFO @ Sat, 03 Apr 2021 06:49:33: 8000000 INFO @ Sat, 03 Apr 2021 06:49:34: 13000000 INFO @ Sat, 03 Apr 2021 06:49:39: 19000000 INFO @ Sat, 03 Apr 2021 06:49:40: 9000000 INFO @ Sat, 03 Apr 2021 06:49:41: 14000000 INFO @ Sat, 03 Apr 2021 06:49:46: 20000000 INFO @ Sat, 03 Apr 2021 06:49:48: 10000000 INFO @ Sat, 03 Apr 2021 06:49:49: 15000000 INFO @ Sat, 03 Apr 2021 06:49:53: 21000000 INFO @ Sat, 03 Apr 2021 06:49:54: #1 tag size is determined as 47 bps INFO @ Sat, 03 Apr 2021 06:49:54: #1 tag size = 47 INFO @ Sat, 03 Apr 2021 06:49:54: #1 total tags in treatment: 21054666 INFO @ Sat, 03 Apr 2021 06:49:54: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:49:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:49:54: #1 tags after filtering in treatment: 21054666 INFO @ Sat, 03 Apr 2021 06:49:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:49:54: #1 finished! INFO @ Sat, 03 Apr 2021 06:49:54: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:49:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:49:56: 11000000 INFO @ Sat, 03 Apr 2021 06:49:56: #2 number of paired peaks: 253 WARNING @ Sat, 03 Apr 2021 06:49:56: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Sat, 03 Apr 2021 06:49:56: start model_add_line... INFO @ Sat, 03 Apr 2021 06:49:56: start X-correlation... INFO @ Sat, 03 Apr 2021 06:49:56: end of X-cor INFO @ Sat, 03 Apr 2021 06:49:56: #2 finished! INFO @ Sat, 03 Apr 2021 06:49:56: #2 predicted fragment length is 60 bps INFO @ Sat, 03 Apr 2021 06:49:56: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sat, 03 Apr 2021 06:49:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.05_model.r WARNING @ Sat, 03 Apr 2021 06:49:56: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:49:56: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sat, 03 Apr 2021 06:49:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:49:56: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:49:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:49:58: 16000000 INFO @ Sat, 03 Apr 2021 06:50:04: 12000000 INFO @ Sat, 03 Apr 2021 06:50:06: 17000000 INFO @ Sat, 03 Apr 2021 06:50:13: 13000000 INFO @ Sat, 03 Apr 2021 06:50:15: 18000000 INFO @ Sat, 03 Apr 2021 06:50:23: 14000000 INFO @ Sat, 03 Apr 2021 06:50:24: 19000000 INFO @ Sat, 03 Apr 2021 06:50:32: 15000000 INFO @ Sat, 03 Apr 2021 06:50:35: 20000000 INFO @ Sat, 03 Apr 2021 06:50:41: 16000000 INFO @ Sat, 03 Apr 2021 06:50:42: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:50:45: 21000000 INFO @ Sat, 03 Apr 2021 06:50:45: #1 tag size is determined as 47 bps INFO @ Sat, 03 Apr 2021 06:50:45: #1 tag size = 47 INFO @ Sat, 03 Apr 2021 06:50:45: #1 total tags in treatment: 21054666 INFO @ Sat, 03 Apr 2021 06:50:45: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:50:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:50:46: #1 tags after filtering in treatment: 21054666 INFO @ Sat, 03 Apr 2021 06:50:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:50:46: #1 finished! INFO @ Sat, 03 Apr 2021 06:50:46: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:50:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:50:47: #2 number of paired peaks: 253 WARNING @ Sat, 03 Apr 2021 06:50:47: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Sat, 03 Apr 2021 06:50:47: start model_add_line... INFO @ Sat, 03 Apr 2021 06:50:48: start X-correlation... INFO @ Sat, 03 Apr 2021 06:50:48: end of X-cor INFO @ Sat, 03 Apr 2021 06:50:48: #2 finished! INFO @ Sat, 03 Apr 2021 06:50:48: #2 predicted fragment length is 60 bps INFO @ Sat, 03 Apr 2021 06:50:48: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sat, 03 Apr 2021 06:50:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.10_model.r WARNING @ Sat, 03 Apr 2021 06:50:48: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:50:48: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sat, 03 Apr 2021 06:50:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:50:48: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:50:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:50:51: 17000000 INFO @ Sat, 03 Apr 2021 06:51:00: 18000000 INFO @ Sat, 03 Apr 2021 06:51:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:51:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:51:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.05_summits.bed INFO @ Sat, 03 Apr 2021 06:51:08: Done! pass1 - making usageList (7 chroms): 13 millis pass2 - checking and writing primary data (18099 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:51:09: 19000000 INFO @ Sat, 03 Apr 2021 06:51:17: 20000000 INFO @ Sat, 03 Apr 2021 06:51:25: 21000000 INFO @ Sat, 03 Apr 2021 06:51:26: #1 tag size is determined as 47 bps INFO @ Sat, 03 Apr 2021 06:51:26: #1 tag size = 47 INFO @ Sat, 03 Apr 2021 06:51:26: #1 total tags in treatment: 21054666 INFO @ Sat, 03 Apr 2021 06:51:26: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:51:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:51:26: #1 tags after filtering in treatment: 21054666 INFO @ Sat, 03 Apr 2021 06:51:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:51:26: #1 finished! INFO @ Sat, 03 Apr 2021 06:51:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:51:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:51:28: #2 number of paired peaks: 253 WARNING @ Sat, 03 Apr 2021 06:51:28: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Sat, 03 Apr 2021 06:51:28: start model_add_line... INFO @ Sat, 03 Apr 2021 06:51:28: start X-correlation... INFO @ Sat, 03 Apr 2021 06:51:28: end of X-cor INFO @ Sat, 03 Apr 2021 06:51:28: #2 finished! INFO @ Sat, 03 Apr 2021 06:51:28: #2 predicted fragment length is 60 bps INFO @ Sat, 03 Apr 2021 06:51:28: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sat, 03 Apr 2021 06:51:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.20_model.r WARNING @ Sat, 03 Apr 2021 06:51:28: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:51:28: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sat, 03 Apr 2021 06:51:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:51:28: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:51:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:51:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:51:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:51:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:51:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.10_summits.bed INFO @ Sat, 03 Apr 2021 06:51:54: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (10860 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:52:10: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:52:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:52:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:52:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082401/SRX4082401.20_summits.bed INFO @ Sat, 03 Apr 2021 06:52:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3989 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。