Job ID = 10165985 SRX = SRX8331162 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: 00:11:25 34618852 reads; of these: 34618852 (100.00%) were unpaired; of these: 2947405 (8.51%) aligned 0 times 26086530 (75.35%) aligned exactly 1 time 5584917 (16.13%) aligned >1 times 91.49% overall alignment rate Time searching: 00:11:25 Overall time: 00:11:25 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] 24496688 / 31671447 = 0.7735 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 20:38:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.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 20:38:59: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:38:59: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:39:07: 1000000 INFO @ Thu, 08 Oct 2020 20:39:14: 2000000 INFO @ Thu, 08 Oct 2020 20:39:21: 3000000 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 20:39:28: 4000000 INFO @ Thu, 08 Oct 2020 20:39:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.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 20:39:30: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:39:30: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:39:36: 5000000 INFO @ Thu, 08 Oct 2020 20:39:39: 1000000 INFO @ Thu, 08 Oct 2020 20:39:44: 6000000 INFO @ Thu, 08 Oct 2020 20:39:46: 2000000 INFO @ Thu, 08 Oct 2020 20:39:52: 7000000 INFO @ Thu, 08 Oct 2020 20:39:54: #1 tag size is determined as 68 bps INFO @ Thu, 08 Oct 2020 20:39:54: #1 tag size = 68 INFO @ Thu, 08 Oct 2020 20:39:54: #1 total tags in treatment: 7174759 INFO @ Thu, 08 Oct 2020 20:39:54: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:39:54: #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 20:39:54: #1 tags after filtering in treatment: 7174759 INFO @ Thu, 08 Oct 2020 20:39:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:39:54: #1 finished! INFO @ Thu, 08 Oct 2020 20:39:54: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:39:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:39:54: #2 number of paired peaks: 823 WARNING @ Thu, 08 Oct 2020 20:39:54: Fewer paired peaks (823) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 823 pairs to build model! INFO @ Thu, 08 Oct 2020 20:39:54: start model_add_line... INFO @ Thu, 08 Oct 2020 20:39:54: start X-correlation... INFO @ Thu, 08 Oct 2020 20:39:54: end of X-cor INFO @ Thu, 08 Oct 2020 20:39:54: #2 finished! INFO @ Thu, 08 Oct 2020 20:39:54: #2 predicted fragment length is 74 bps INFO @ Thu, 08 Oct 2020 20:39:54: #2 alternative fragment length(s) may be 4,74 bps INFO @ Thu, 08 Oct 2020 20:39:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.05_model.r WARNING @ Thu, 08 Oct 2020 20:39:54: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:39:54: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Thu, 08 Oct 2020 20:39:54: #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 20:39:54: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:39:54: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:39:54: 3000000 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 20:40:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.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 20:40:00: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:40:00: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:40:01: 4000000 INFO @ Thu, 08 Oct 2020 20:40:07: 1000000 INFO @ Thu, 08 Oct 2020 20:40:08: 5000000 INFO @ Thu, 08 Oct 2020 20:40:10: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:40:14: 2000000 INFO @ Thu, 08 Oct 2020 20:40:15: 6000000 INFO @ Thu, 08 Oct 2020 20:40:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:40:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:40:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.05_summits.bed INFO @ Thu, 08 Oct 2020 20:40:18: Done! INFO @ Thu, 08 Oct 2020 20:40:21: 3000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1647 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:40:22: 7000000 INFO @ Thu, 08 Oct 2020 20:40:23: #1 tag size is determined as 68 bps INFO @ Thu, 08 Oct 2020 20:40:23: #1 tag size = 68 INFO @ Thu, 08 Oct 2020 20:40:23: #1 total tags in treatment: 7174759 INFO @ Thu, 08 Oct 2020 20:40:23: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:40:23: #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 20:40:23: #1 tags after filtering in treatment: 7174759 INFO @ Thu, 08 Oct 2020 20:40:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:40:23: #1 finished! INFO @ Thu, 08 Oct 2020 20:40:23: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:40:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:40:24: #2 number of paired peaks: 823 WARNING @ Thu, 08 Oct 2020 20:40:24: Fewer paired peaks (823) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 823 pairs to build model! INFO @ Thu, 08 Oct 2020 20:40:24: start model_add_line... INFO @ Thu, 08 Oct 2020 20:40:24: start X-correlation... INFO @ Thu, 08 Oct 2020 20:40:24: end of X-cor INFO @ Thu, 08 Oct 2020 20:40:24: #2 finished! INFO @ Thu, 08 Oct 2020 20:40:24: #2 predicted fragment length is 74 bps INFO @ Thu, 08 Oct 2020 20:40:24: #2 alternative fragment length(s) may be 4,74 bps INFO @ Thu, 08 Oct 2020 20:40:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.10_model.r WARNING @ Thu, 08 Oct 2020 20:40:24: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:40:24: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Thu, 08 Oct 2020 20:40:24: #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 20:40:24: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:40:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:40:27: 4000000 INFO @ Thu, 08 Oct 2020 20:40:34: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:40:41: 6000000 INFO @ Thu, 08 Oct 2020 20:40:41: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:40:47: 7000000 INFO @ Thu, 08 Oct 2020 20:40:48: #1 tag size is determined as 68 bps INFO @ Thu, 08 Oct 2020 20:40:48: #1 tag size = 68 INFO @ Thu, 08 Oct 2020 20:40:48: #1 total tags in treatment: 7174759 INFO @ Thu, 08 Oct 2020 20:40:48: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:40:48: #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 20:40:48: #1 tags after filtering in treatment: 7174759 INFO @ Thu, 08 Oct 2020 20:40:48: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:40:48: #1 finished! INFO @ Thu, 08 Oct 2020 20:40:48: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:40:48: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:40:49: #2 number of paired peaks: 823 WARNING @ Thu, 08 Oct 2020 20:40:49: Fewer paired peaks (823) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 823 pairs to build model! INFO @ Thu, 08 Oct 2020 20:40:49: start model_add_line... INFO @ Thu, 08 Oct 2020 20:40:49: start X-correlation... INFO @ Thu, 08 Oct 2020 20:40:49: end of X-cor INFO @ Thu, 08 Oct 2020 20:40:49: #2 finished! INFO @ Thu, 08 Oct 2020 20:40:49: #2 predicted fragment length is 74 bps INFO @ Thu, 08 Oct 2020 20:40:49: #2 alternative fragment length(s) may be 4,74 bps INFO @ Thu, 08 Oct 2020 20:40:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.20_model.r WARNING @ Thu, 08 Oct 2020 20:40:49: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 20:40:49: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Thu, 08 Oct 2020 20:40:49: #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 20:40:49: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:40:49: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:40:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:40:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:40:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.10_summits.bed INFO @ Thu, 08 Oct 2020 20:40:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (841 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 20:41:06: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:41:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:41:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:41:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8331162/SRX8331162.20_summits.bed INFO @ Thu, 08 Oct 2020 20:41:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (395 records, 4 fields): 2 millis CompletedMACS2peakCalling