Job ID = 10165892 SRX = SRX6799186 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:12 35279189 reads; of these: 35279189 (100.00%) were unpaired; of these: 1632973 (4.63%) aligned 0 times 26488916 (75.08%) aligned exactly 1 time 7157300 (20.29%) aligned >1 times 95.37% overall alignment rate Time searching: 00:08:12 Overall time: 00:08:12 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] 9685544 / 33646216 = 0.2879 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:21:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.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, 08 Oct 2020 20:21:55: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:21:55: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:22:00: 1000000 INFO @ Thu, 08 Oct 2020 20:22:05: 2000000 INFO @ Thu, 08 Oct 2020 20:22:10: 3000000 INFO @ Thu, 08 Oct 2020 20:22:15: 4000000 INFO @ Thu, 08 Oct 2020 20:22:20: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:22:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.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, 08 Oct 2020 20:22:25: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:22:25: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:22:25: 6000000 INFO @ Thu, 08 Oct 2020 20:22:30: 1000000 INFO @ Thu, 08 Oct 2020 20:22:30: 7000000 INFO @ Thu, 08 Oct 2020 20:22:35: 2000000 INFO @ Thu, 08 Oct 2020 20:22:35: 8000000 INFO @ Thu, 08 Oct 2020 20:22:40: 3000000 INFO @ Thu, 08 Oct 2020 20:22:40: 9000000 INFO @ Thu, 08 Oct 2020 20:22:45: 4000000 INFO @ Thu, 08 Oct 2020 20:22:45: 10000000 INFO @ Thu, 08 Oct 2020 20:22:50: 5000000 INFO @ Thu, 08 Oct 2020 20:22:51: 11000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 20:22:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.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, 08 Oct 2020 20:22:55: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:22:55: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:22:56: 6000000 INFO @ Thu, 08 Oct 2020 20:22:56: 12000000 INFO @ Thu, 08 Oct 2020 20:23:00: 1000000 INFO @ Thu, 08 Oct 2020 20:23:01: 7000000 INFO @ Thu, 08 Oct 2020 20:23:01: 13000000 INFO @ Thu, 08 Oct 2020 20:23:05: 2000000 INFO @ Thu, 08 Oct 2020 20:23:06: 8000000 INFO @ Thu, 08 Oct 2020 20:23:06: 14000000 INFO @ Thu, 08 Oct 2020 20:23:10: 3000000 INFO @ Thu, 08 Oct 2020 20:23:11: 9000000 INFO @ Thu, 08 Oct 2020 20:23:11: 15000000 INFO @ Thu, 08 Oct 2020 20:23:16: 4000000 INFO @ Thu, 08 Oct 2020 20:23:16: 10000000 INFO @ Thu, 08 Oct 2020 20:23:17: 16000000 INFO @ Thu, 08 Oct 2020 20:23:21: 5000000 INFO @ Thu, 08 Oct 2020 20:23:22: 11000000 INFO @ Thu, 08 Oct 2020 20:23:23: 17000000 INFO @ Thu, 08 Oct 2020 20:23:26: 6000000 INFO @ Thu, 08 Oct 2020 20:23:27: 12000000 INFO @ Thu, 08 Oct 2020 20:23:28: 18000000 INFO @ Thu, 08 Oct 2020 20:23:32: 7000000 INFO @ Thu, 08 Oct 2020 20:23:32: 13000000 INFO @ Thu, 08 Oct 2020 20:23:33: 19000000 INFO @ Thu, 08 Oct 2020 20:23:37: 8000000 INFO @ Thu, 08 Oct 2020 20:23:37: 14000000 INFO @ Thu, 08 Oct 2020 20:23:39: 20000000 INFO @ Thu, 08 Oct 2020 20:23:42: 9000000 INFO @ Thu, 08 Oct 2020 20:23:43: 15000000 INFO @ Thu, 08 Oct 2020 20:23:44: 21000000 INFO @ Thu, 08 Oct 2020 20:23:47: 10000000 INFO @ Thu, 08 Oct 2020 20:23:48: 16000000 INFO @ Thu, 08 Oct 2020 20:23:49: 22000000 INFO @ Thu, 08 Oct 2020 20:23:53: 11000000 INFO @ Thu, 08 Oct 2020 20:23:53: 17000000 INFO @ Thu, 08 Oct 2020 20:23:54: 23000000 INFO @ Thu, 08 Oct 2020 20:23:58: 12000000 INFO @ Thu, 08 Oct 2020 20:23:58: 18000000 INFO @ Thu, 08 Oct 2020 20:24:00: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:24:00: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:24:00: #1 total tags in treatment: 23960672 INFO @ Thu, 08 Oct 2020 20:24:00: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:24:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:24:00: #1 tags after filtering in treatment: 23960672 INFO @ Thu, 08 Oct 2020 20:24:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:24:00: #1 finished! INFO @ Thu, 08 Oct 2020 20:24:00: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:24:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:24:01: #2 number of paired peaks: 158 WARNING @ Thu, 08 Oct 2020 20:24:01: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Thu, 08 Oct 2020 20:24:01: start model_add_line... INFO @ Thu, 08 Oct 2020 20:24:02: start X-correlation... INFO @ Thu, 08 Oct 2020 20:24:02: end of X-cor INFO @ Thu, 08 Oct 2020 20:24:02: #2 finished! INFO @ Thu, 08 Oct 2020 20:24:02: #2 predicted fragment length is 52 bps INFO @ Thu, 08 Oct 2020 20:24:02: #2 alternative fragment length(s) may be 3,52,101,103,116,198 bps INFO @ Thu, 08 Oct 2020 20:24:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.05_model.r WARNING @ Thu, 08 Oct 2020 20:24:02: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:24:02: #2 You may need to consider one of the other alternative d(s): 3,52,101,103,116,198 WARNING @ Thu, 08 Oct 2020 20:24:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:24:02: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:24:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:24:03: 13000000 INFO @ Thu, 08 Oct 2020 20:24:04: 19000000 INFO @ Thu, 08 Oct 2020 20:24:08: 14000000 INFO @ Thu, 08 Oct 2020 20:24:09: 20000000 INFO @ Thu, 08 Oct 2020 20:24:13: 15000000 INFO @ Thu, 08 Oct 2020 20:24:14: 21000000 INFO @ Thu, 08 Oct 2020 20:24:18: 16000000 INFO @ Thu, 08 Oct 2020 20:24:19: 22000000 INFO @ Thu, 08 Oct 2020 20:24:24: 17000000 INFO @ Thu, 08 Oct 2020 20:24:24: 23000000 INFO @ Thu, 08 Oct 2020 20:24:29: 18000000 INFO @ Thu, 08 Oct 2020 20:24:29: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:24:29: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:24:29: #1 total tags in treatment: 23960672 INFO @ Thu, 08 Oct 2020 20:24:29: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:24:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:24:30: #1 tags after filtering in treatment: 23960672 INFO @ Thu, 08 Oct 2020 20:24:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:24:30: #1 finished! INFO @ Thu, 08 Oct 2020 20:24:30: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:24:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:24:31: #2 number of paired peaks: 158 WARNING @ Thu, 08 Oct 2020 20:24:31: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Thu, 08 Oct 2020 20:24:31: start model_add_line... INFO @ Thu, 08 Oct 2020 20:24:31: start X-correlation... INFO @ Thu, 08 Oct 2020 20:24:31: end of X-cor INFO @ Thu, 08 Oct 2020 20:24:31: #2 finished! INFO @ Thu, 08 Oct 2020 20:24:31: #2 predicted fragment length is 52 bps INFO @ Thu, 08 Oct 2020 20:24:31: #2 alternative fragment length(s) may be 3,52,101,103,116,198 bps INFO @ Thu, 08 Oct 2020 20:24:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.10_model.r WARNING @ Thu, 08 Oct 2020 20:24:31: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:24:31: #2 You may need to consider one of the other alternative d(s): 3,52,101,103,116,198 WARNING @ Thu, 08 Oct 2020 20:24:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:24:31: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:24:31: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:24:34: 19000000 INFO @ Thu, 08 Oct 2020 20:24:39: 20000000 INFO @ Thu, 08 Oct 2020 20:24:41: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:24:44: 21000000 INFO @ Thu, 08 Oct 2020 20:24:49: 22000000 INFO @ Thu, 08 Oct 2020 20:24:54: 23000000 INFO @ Thu, 08 Oct 2020 20:24:59: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:24:59: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:24:59: #1 total tags in treatment: 23960672 INFO @ Thu, 08 Oct 2020 20:24:59: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:24:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 20:24:59: #1 tags after filtering in treatment: 23960672 INFO @ Thu, 08 Oct 2020 20:24:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:24:59: #1 finished! INFO @ Thu, 08 Oct 2020 20:24:59: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:24:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:25:00: #2 number of paired peaks: 158 WARNING @ Thu, 08 Oct 2020 20:25:00: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Thu, 08 Oct 2020 20:25:00: start model_add_line... INFO @ Thu, 08 Oct 2020 20:25:01: start X-correlation... INFO @ Thu, 08 Oct 2020 20:25:01: end of X-cor INFO @ Thu, 08 Oct 2020 20:25:01: #2 finished! INFO @ Thu, 08 Oct 2020 20:25:01: #2 predicted fragment length is 52 bps INFO @ Thu, 08 Oct 2020 20:25:01: #2 alternative fragment length(s) may be 3,52,101,103,116,198 bps INFO @ Thu, 08 Oct 2020 20:25:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.20_model.r WARNING @ Thu, 08 Oct 2020 20:25:01: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:25:01: #2 You may need to consider one of the other alternative d(s): 3,52,101,103,116,198 WARNING @ Thu, 08 Oct 2020 20:25:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:25:01: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:25:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:25:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:25:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:25:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.05_summits.bed INFO @ Thu, 08 Oct 2020 20:25:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (9542 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:25:10: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:25:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:25:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:25:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.10_summits.bed INFO @ Thu, 08 Oct 2020 20:25:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2696 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:25:40: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:26:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:26:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:26:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799186/SRX6799186.20_summits.bed INFO @ Thu, 08 Oct 2020 20:26:01: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (391 records, 4 fields): 2 millis CompletedMACS2peakCalling