Job ID = 10165886 SRX = SRX6799185 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: 00:07:52 34054065 reads; of these: 34054065 (100.00%) were unpaired; of these: 2234955 (6.56%) aligned 0 times 24303661 (71.37%) aligned exactly 1 time 7515449 (22.07%) aligned >1 times 93.44% overall alignment rate Time searching: 00:07:52 Overall time: 00:07:52 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] 8937090 / 31819110 = 0.2809 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 20:20:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.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 20:20:58: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:20:58: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:21:03: 1000000 INFO @ Thu, 08 Oct 2020 20:21:08: 2000000 INFO @ Thu, 08 Oct 2020 20:21:13: 3000000 INFO @ Thu, 08 Oct 2020 20:21:18: 4000000 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 20:21:22: 5000000 INFO @ Thu, 08 Oct 2020 20:21:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.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 20:21:26: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:21:26: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:21:27: 6000000 INFO @ Thu, 08 Oct 2020 20:21:31: 1000000 INFO @ Thu, 08 Oct 2020 20:21:32: 7000000 INFO @ Thu, 08 Oct 2020 20:21:36: 2000000 INFO @ Thu, 08 Oct 2020 20:21:37: 8000000 INFO @ Thu, 08 Oct 2020 20:21:41: 3000000 INFO @ Thu, 08 Oct 2020 20:21:42: 9000000 INFO @ Thu, 08 Oct 2020 20:21:46: 4000000 INFO @ Thu, 08 Oct 2020 20:21:47: 10000000 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 20:21:51: 5000000 INFO @ Thu, 08 Oct 2020 20:21:52: 11000000 INFO @ Thu, 08 Oct 2020 20:21:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.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 20:21:54: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:21:54: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:21:56: 6000000 INFO @ Thu, 08 Oct 2020 20:21:57: 12000000 INFO @ Thu, 08 Oct 2020 20:21:59: 1000000 INFO @ Thu, 08 Oct 2020 20:22:01: 7000000 INFO @ Thu, 08 Oct 2020 20:22:02: 13000000 INFO @ Thu, 08 Oct 2020 20:22:04: 2000000 INFO @ Thu, 08 Oct 2020 20:22:06: 8000000 INFO @ Thu, 08 Oct 2020 20:22:07: 14000000 INFO @ Thu, 08 Oct 2020 20:22:09: 3000000 INFO @ Thu, 08 Oct 2020 20:22:11: 9000000 INFO @ Thu, 08 Oct 2020 20:22:12: 15000000 INFO @ Thu, 08 Oct 2020 20:22:14: 4000000 INFO @ Thu, 08 Oct 2020 20:22:16: 10000000 INFO @ Thu, 08 Oct 2020 20:22:17: 16000000 INFO @ Thu, 08 Oct 2020 20:22:19: 5000000 INFO @ Thu, 08 Oct 2020 20:22:21: 11000000 INFO @ Thu, 08 Oct 2020 20:22:22: 17000000 INFO @ Thu, 08 Oct 2020 20:22:24: 6000000 INFO @ Thu, 08 Oct 2020 20:22:26: 12000000 INFO @ Thu, 08 Oct 2020 20:22:27: 18000000 INFO @ Thu, 08 Oct 2020 20:22:29: 7000000 INFO @ Thu, 08 Oct 2020 20:22:31: 13000000 INFO @ Thu, 08 Oct 2020 20:22:31: 19000000 INFO @ Thu, 08 Oct 2020 20:22:34: 8000000 INFO @ Thu, 08 Oct 2020 20:22:36: 14000000 INFO @ Thu, 08 Oct 2020 20:22:36: 20000000 INFO @ Thu, 08 Oct 2020 20:22:39: 9000000 INFO @ Thu, 08 Oct 2020 20:22:41: 15000000 INFO @ Thu, 08 Oct 2020 20:22:41: 21000000 INFO @ Thu, 08 Oct 2020 20:22:44: 10000000 INFO @ Thu, 08 Oct 2020 20:22:46: 16000000 INFO @ Thu, 08 Oct 2020 20:22:46: 22000000 INFO @ Thu, 08 Oct 2020 20:22:49: 11000000 INFO @ Thu, 08 Oct 2020 20:22:51: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:22:51: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:22:51: #1 total tags in treatment: 22882020 INFO @ Thu, 08 Oct 2020 20:22:51: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:22:51: #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 20:22:51: 17000000 INFO @ Thu, 08 Oct 2020 20:22:51: #1 tags after filtering in treatment: 22882020 INFO @ Thu, 08 Oct 2020 20:22:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:22:51: #1 finished! INFO @ Thu, 08 Oct 2020 20:22:51: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:22:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:22:52: #2 number of paired peaks: 219 WARNING @ Thu, 08 Oct 2020 20:22:52: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Thu, 08 Oct 2020 20:22:52: start model_add_line... INFO @ Thu, 08 Oct 2020 20:22:53: start X-correlation... INFO @ Thu, 08 Oct 2020 20:22:53: end of X-cor INFO @ Thu, 08 Oct 2020 20:22:53: #2 finished! INFO @ Thu, 08 Oct 2020 20:22:53: #2 predicted fragment length is 59 bps INFO @ Thu, 08 Oct 2020 20:22:53: #2 alternative fragment length(s) may be 2,50,59,85 bps INFO @ Thu, 08 Oct 2020 20:22:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.05_model.r WARNING @ Thu, 08 Oct 2020 20:22:53: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:22:53: #2 You may need to consider one of the other alternative d(s): 2,50,59,85 WARNING @ Thu, 08 Oct 2020 20:22:53: #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 20:22:53: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:22:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:22:54: 12000000 INFO @ Thu, 08 Oct 2020 20:22:56: 18000000 INFO @ Thu, 08 Oct 2020 20:22:59: 13000000 INFO @ Thu, 08 Oct 2020 20:23:01: 19000000 INFO @ Thu, 08 Oct 2020 20:23:03: 14000000 INFO @ Thu, 08 Oct 2020 20:23:05: 20000000 INFO @ Thu, 08 Oct 2020 20:23:08: 15000000 INFO @ Thu, 08 Oct 2020 20:23:10: 21000000 INFO @ Thu, 08 Oct 2020 20:23:13: 16000000 INFO @ Thu, 08 Oct 2020 20:23:15: 22000000 INFO @ Thu, 08 Oct 2020 20:23:18: 17000000 INFO @ Thu, 08 Oct 2020 20:23:20: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:23:20: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:23:20: #1 total tags in treatment: 22882020 INFO @ Thu, 08 Oct 2020 20:23:20: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:23:20: #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 20:23:20: #1 tags after filtering in treatment: 22882020 INFO @ Thu, 08 Oct 2020 20:23:20: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:23:20: #1 finished! INFO @ Thu, 08 Oct 2020 20:23:20: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:23:20: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:23:21: #2 number of paired peaks: 219 WARNING @ Thu, 08 Oct 2020 20:23:21: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Thu, 08 Oct 2020 20:23:21: start model_add_line... INFO @ Thu, 08 Oct 2020 20:23:22: start X-correlation... INFO @ Thu, 08 Oct 2020 20:23:22: end of X-cor INFO @ Thu, 08 Oct 2020 20:23:22: #2 finished! INFO @ Thu, 08 Oct 2020 20:23:22: #2 predicted fragment length is 59 bps INFO @ Thu, 08 Oct 2020 20:23:22: #2 alternative fragment length(s) may be 2,50,59,85 bps INFO @ Thu, 08 Oct 2020 20:23:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.10_model.r WARNING @ Thu, 08 Oct 2020 20:23:22: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:23:22: #2 You may need to consider one of the other alternative d(s): 2,50,59,85 WARNING @ Thu, 08 Oct 2020 20:23:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 20:23:22: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:23:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:23:23: 18000000 INFO @ Thu, 08 Oct 2020 20:23:28: 19000000 INFO @ Thu, 08 Oct 2020 20:23:32: 20000000 INFO @ Thu, 08 Oct 2020 20:23:34: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:23:37: 21000000 INFO @ Thu, 08 Oct 2020 20:23:42: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:23:46: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:23:46: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:23:46: #1 total tags in treatment: 22882020 INFO @ Thu, 08 Oct 2020 20:23:46: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:23:46: #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 20:23:46: #1 tags after filtering in treatment: 22882020 INFO @ Thu, 08 Oct 2020 20:23:46: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:23:46: #1 finished! INFO @ Thu, 08 Oct 2020 20:23:46: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:23:46: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:23:48: #2 number of paired peaks: 219 WARNING @ Thu, 08 Oct 2020 20:23:48: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Thu, 08 Oct 2020 20:23:48: start model_add_line... INFO @ Thu, 08 Oct 2020 20:23:48: start X-correlation... INFO @ Thu, 08 Oct 2020 20:23:48: end of X-cor INFO @ Thu, 08 Oct 2020 20:23:48: #2 finished! INFO @ Thu, 08 Oct 2020 20:23:48: #2 predicted fragment length is 59 bps INFO @ Thu, 08 Oct 2020 20:23:48: #2 alternative fragment length(s) may be 2,50,59,85 bps INFO @ Thu, 08 Oct 2020 20:23:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.20_model.r WARNING @ Thu, 08 Oct 2020 20:23:48: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:23:48: #2 You may need to consider one of the other alternative d(s): 2,50,59,85 WARNING @ Thu, 08 Oct 2020 20:23:48: #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 20:23:48: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:23:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:23:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:23:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:23:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.05_summits.bed INFO @ Thu, 08 Oct 2020 20:23:55: Done! INFO @ Thu, 08 Oct 2020 20:24:03: #3 Call peaks for each chromosome... pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (9788 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:24:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:24:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:24:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.10_summits.bed INFO @ Thu, 08 Oct 2020 20:24:24: Done! BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:24:26: #3 Call peaks for each chromosome... pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (3244 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:24:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:24:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:24:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX6799185/SRX6799185.20_summits.bed INFO @ Thu, 08 Oct 2020 20:24:46: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (484 records, 4 fields): 3 millis CompletedMACS2peakCalling