Job ID = 6529101 SRX = SRX3043413 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:08 15936085 reads; of these: 15936085 (100.00%) were unpaired; of these: 230121 (1.44%) aligned 0 times 13474024 (84.55%) aligned exactly 1 time 2231940 (14.01%) aligned >1 times 98.56% overall alignment rate Time searching: 00:05:09 Overall time: 00:05:09 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] 1685410 / 15705964 = 0.1073 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 @ Tue, 30 Jun 2020 01:28:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.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 @ Tue, 30 Jun 2020 01:28:22: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:28:22: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:28:28: 1000000 INFO @ Tue, 30 Jun 2020 01:28:34: 2000000 INFO @ Tue, 30 Jun 2020 01:28:41: 3000000 INFO @ Tue, 30 Jun 2020 01:28:47: 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 @ Tue, 30 Jun 2020 01:28:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.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 @ Tue, 30 Jun 2020 01:28:52: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:28:52: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:28:53: 5000000 INFO @ Tue, 30 Jun 2020 01:29:00: 1000000 INFO @ Tue, 30 Jun 2020 01:29:00: 6000000 INFO @ Tue, 30 Jun 2020 01:29:07: 7000000 INFO @ Tue, 30 Jun 2020 01:29:08: 2000000 INFO @ Tue, 30 Jun 2020 01:29:14: 8000000 INFO @ Tue, 30 Jun 2020 01:29:15: 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 @ Tue, 30 Jun 2020 01:29:21: 9000000 INFO @ Tue, 30 Jun 2020 01:29:21: 4000000 INFO @ Tue, 30 Jun 2020 01:29:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.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 @ Tue, 30 Jun 2020 01:29:22: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:29:22: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:29:28: 10000000 INFO @ Tue, 30 Jun 2020 01:29:28: 5000000 INFO @ Tue, 30 Jun 2020 01:29:29: 1000000 INFO @ Tue, 30 Jun 2020 01:29:35: 11000000 INFO @ Tue, 30 Jun 2020 01:29:35: 6000000 INFO @ Tue, 30 Jun 2020 01:29:36: 2000000 INFO @ Tue, 30 Jun 2020 01:29:42: 12000000 INFO @ Tue, 30 Jun 2020 01:29:42: 7000000 INFO @ Tue, 30 Jun 2020 01:29:44: 3000000 INFO @ Tue, 30 Jun 2020 01:29:49: 13000000 INFO @ Tue, 30 Jun 2020 01:29:49: 8000000 INFO @ Tue, 30 Jun 2020 01:29:51: 4000000 INFO @ Tue, 30 Jun 2020 01:29:56: 14000000 INFO @ Tue, 30 Jun 2020 01:29:56: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:29:56: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:29:56: #1 total tags in treatment: 14020554 INFO @ Tue, 30 Jun 2020 01:29:56: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:29:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:29:56: #1 tags after filtering in treatment: 14020554 INFO @ Tue, 30 Jun 2020 01:29:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:29:56: #1 finished! INFO @ Tue, 30 Jun 2020 01:29:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:29:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:29:56: 9000000 INFO @ Tue, 30 Jun 2020 01:29:57: #2 number of paired peaks: 134 WARNING @ Tue, 30 Jun 2020 01:29:57: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Tue, 30 Jun 2020 01:29:57: start model_add_line... INFO @ Tue, 30 Jun 2020 01:29:57: start X-correlation... INFO @ Tue, 30 Jun 2020 01:29:57: end of X-cor INFO @ Tue, 30 Jun 2020 01:29:57: #2 finished! INFO @ Tue, 30 Jun 2020 01:29:57: #2 predicted fragment length is 55 bps INFO @ Tue, 30 Jun 2020 01:29:57: #2 alternative fragment length(s) may be 1,55,492,509 bps INFO @ Tue, 30 Jun 2020 01:29:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.05_model.r WARNING @ Tue, 30 Jun 2020 01:29:57: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:29:57: #2 You may need to consider one of the other alternative d(s): 1,55,492,509 WARNING @ Tue, 30 Jun 2020 01:29:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:29:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:29:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:29:58: 5000000 INFO @ Tue, 30 Jun 2020 01:30:03: 10000000 INFO @ Tue, 30 Jun 2020 01:30:06: 6000000 INFO @ Tue, 30 Jun 2020 01:30:09: 11000000 INFO @ Tue, 30 Jun 2020 01:30:13: 7000000 INFO @ Tue, 30 Jun 2020 01:30:16: 12000000 INFO @ Tue, 30 Jun 2020 01:30:20: 8000000 INFO @ Tue, 30 Jun 2020 01:30:21: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:30:22: 13000000 INFO @ Tue, 30 Jun 2020 01:30:27: 9000000 INFO @ Tue, 30 Jun 2020 01:30:29: 14000000 INFO @ Tue, 30 Jun 2020 01:30:29: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:30:29: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:30:29: #1 total tags in treatment: 14020554 INFO @ Tue, 30 Jun 2020 01:30:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:30:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:30:29: #1 tags after filtering in treatment: 14020554 INFO @ Tue, 30 Jun 2020 01:30:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:30:29: #1 finished! INFO @ Tue, 30 Jun 2020 01:30:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:30:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:30:30: #2 number of paired peaks: 134 WARNING @ Tue, 30 Jun 2020 01:30:30: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Tue, 30 Jun 2020 01:30:30: start model_add_line... INFO @ Tue, 30 Jun 2020 01:30:30: start X-correlation... INFO @ Tue, 30 Jun 2020 01:30:30: end of X-cor INFO @ Tue, 30 Jun 2020 01:30:30: #2 finished! INFO @ Tue, 30 Jun 2020 01:30:30: #2 predicted fragment length is 55 bps INFO @ Tue, 30 Jun 2020 01:30:30: #2 alternative fragment length(s) may be 1,55,492,509 bps INFO @ Tue, 30 Jun 2020 01:30:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.10_model.r WARNING @ Tue, 30 Jun 2020 01:30:30: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:30:30: #2 You may need to consider one of the other alternative d(s): 1,55,492,509 WARNING @ Tue, 30 Jun 2020 01:30:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:30:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:30:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:30:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:30:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:30:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.05_summits.bed INFO @ Tue, 30 Jun 2020 01:30:33: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (498 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:30:34: 10000000 INFO @ Tue, 30 Jun 2020 01:30:41: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:30:48: 12000000 INFO @ Tue, 30 Jun 2020 01:30:53: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:30:54: 13000000 INFO @ Tue, 30 Jun 2020 01:31:01: 14000000 INFO @ Tue, 30 Jun 2020 01:31:01: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:31:01: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:31:01: #1 total tags in treatment: 14020554 INFO @ Tue, 30 Jun 2020 01:31:01: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:31:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:31:02: #1 tags after filtering in treatment: 14020554 INFO @ Tue, 30 Jun 2020 01:31:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:31:02: #1 finished! INFO @ Tue, 30 Jun 2020 01:31:02: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:31:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:31:03: #2 number of paired peaks: 134 WARNING @ Tue, 30 Jun 2020 01:31:03: Fewer paired peaks (134) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 134 pairs to build model! INFO @ Tue, 30 Jun 2020 01:31:03: start model_add_line... INFO @ Tue, 30 Jun 2020 01:31:03: start X-correlation... INFO @ Tue, 30 Jun 2020 01:31:03: end of X-cor INFO @ Tue, 30 Jun 2020 01:31:03: #2 finished! INFO @ Tue, 30 Jun 2020 01:31:03: #2 predicted fragment length is 55 bps INFO @ Tue, 30 Jun 2020 01:31:03: #2 alternative fragment length(s) may be 1,55,492,509 bps INFO @ Tue, 30 Jun 2020 01:31:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.20_model.r WARNING @ Tue, 30 Jun 2020 01:31:03: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:31:03: #2 You may need to consider one of the other alternative d(s): 1,55,492,509 WARNING @ Tue, 30 Jun 2020 01:31:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:31:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:31:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:31:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:31:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:31:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.10_summits.bed INFO @ Tue, 30 Jun 2020 01:31:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (257 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:31:26: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:31:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:31:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:31:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3043413/SRX3043413.20_summits.bed INFO @ Tue, 30 Jun 2020 01:31:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (74 records, 4 fields): 2 millis CompletedMACS2peakCalling