Job ID = 14158077 SRX = SRX10040009 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: 00:06:25 23231060 reads; of these: 23231060 (100.00%) were unpaired; of these: 551519 (2.37%) aligned 0 times 19306430 (83.11%) aligned exactly 1 time 3373111 (14.52%) aligned >1 times 97.63% overall alignment rate Time searching: 00:06:25 Overall time: 00:06:25 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 12 files... [bam_rmdupse_core] 5018806 / 22679541 = 0.2213 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 14:23:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.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 @ Wed, 08 Dec 2021 14:23:49: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:23:49: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:23:55: 1000000 INFO @ Wed, 08 Dec 2021 14:24:00: 2000000 INFO @ Wed, 08 Dec 2021 14:24:06: 3000000 INFO @ Wed, 08 Dec 2021 14:24:12: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 14:24:18: 5000000 INFO @ Wed, 08 Dec 2021 14:24:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.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 @ Wed, 08 Dec 2021 14:24:19: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:24:19: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:24:24: 6000000 INFO @ Wed, 08 Dec 2021 14:24:25: 1000000 INFO @ Wed, 08 Dec 2021 14:24:30: 7000000 INFO @ Wed, 08 Dec 2021 14:24:32: 2000000 INFO @ Wed, 08 Dec 2021 14:24:37: 8000000 INFO @ Wed, 08 Dec 2021 14:24:38: 3000000 INFO @ Wed, 08 Dec 2021 14:24:43: 9000000 INFO @ Wed, 08 Dec 2021 14:24:44: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 14:24:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.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 @ Wed, 08 Dec 2021 14:24:49: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:24:49: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:24:49: 10000000 INFO @ Wed, 08 Dec 2021 14:24:51: 5000000 INFO @ Wed, 08 Dec 2021 14:24:56: 1000000 INFO @ Wed, 08 Dec 2021 14:24:56: 11000000 INFO @ Wed, 08 Dec 2021 14:24:58: 6000000 INFO @ Wed, 08 Dec 2021 14:25:03: 12000000 INFO @ Wed, 08 Dec 2021 14:25:03: 2000000 INFO @ Wed, 08 Dec 2021 14:25:05: 7000000 INFO @ Wed, 08 Dec 2021 14:25:10: 13000000 INFO @ Wed, 08 Dec 2021 14:25:10: 3000000 INFO @ Wed, 08 Dec 2021 14:25:12: 8000000 INFO @ Wed, 08 Dec 2021 14:25:16: 14000000 INFO @ Wed, 08 Dec 2021 14:25:17: 4000000 INFO @ Wed, 08 Dec 2021 14:25:18: 9000000 INFO @ Wed, 08 Dec 2021 14:25:23: 15000000 INFO @ Wed, 08 Dec 2021 14:25:24: 5000000 INFO @ Wed, 08 Dec 2021 14:25:25: 10000000 INFO @ Wed, 08 Dec 2021 14:25:30: 16000000 INFO @ Wed, 08 Dec 2021 14:25:31: 6000000 INFO @ Wed, 08 Dec 2021 14:25:32: 11000000 INFO @ Wed, 08 Dec 2021 14:25:36: 17000000 INFO @ Wed, 08 Dec 2021 14:25:37: 7000000 INFO @ Wed, 08 Dec 2021 14:25:39: 12000000 INFO @ Wed, 08 Dec 2021 14:25:40: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:25:40: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:25:40: #1 total tags in treatment: 17660735 INFO @ Wed, 08 Dec 2021 14:25:40: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:25:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:25:41: #1 tags after filtering in treatment: 17660735 INFO @ Wed, 08 Dec 2021 14:25:41: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:25:41: #1 finished! INFO @ Wed, 08 Dec 2021 14:25:41: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:25:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:25:42: #2 number of paired peaks: 105 WARNING @ Wed, 08 Dec 2021 14:25:42: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Wed, 08 Dec 2021 14:25:42: start model_add_line... INFO @ Wed, 08 Dec 2021 14:25:42: start X-correlation... INFO @ Wed, 08 Dec 2021 14:25:42: end of X-cor INFO @ Wed, 08 Dec 2021 14:25:42: #2 finished! INFO @ Wed, 08 Dec 2021 14:25:42: #2 predicted fragment length is 51 bps INFO @ Wed, 08 Dec 2021 14:25:42: #2 alternative fragment length(s) may be 51,555,568,598 bps INFO @ Wed, 08 Dec 2021 14:25:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.05_model.r WARNING @ Wed, 08 Dec 2021 14:25:42: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:25:42: #2 You may need to consider one of the other alternative d(s): 51,555,568,598 WARNING @ Wed, 08 Dec 2021 14:25:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:25:42: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:25:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:25:44: 8000000 INFO @ Wed, 08 Dec 2021 14:25:46: 13000000 INFO @ Wed, 08 Dec 2021 14:25:51: 9000000 INFO @ Wed, 08 Dec 2021 14:25:52: 14000000 INFO @ Wed, 08 Dec 2021 14:25:57: 10000000 INFO @ Wed, 08 Dec 2021 14:25:59: 15000000 INFO @ Wed, 08 Dec 2021 14:26:04: 11000000 INFO @ Wed, 08 Dec 2021 14:26:05: 16000000 INFO @ Wed, 08 Dec 2021 14:26:11: 12000000 INFO @ Wed, 08 Dec 2021 14:26:11: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:26:12: 17000000 INFO @ Wed, 08 Dec 2021 14:26:16: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:26:16: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:26:16: #1 total tags in treatment: 17660735 INFO @ Wed, 08 Dec 2021 14:26:16: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:26:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:26:16: #1 tags after filtering in treatment: 17660735 INFO @ Wed, 08 Dec 2021 14:26:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:26:16: #1 finished! INFO @ Wed, 08 Dec 2021 14:26:16: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:26:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:26:17: 13000000 INFO @ Wed, 08 Dec 2021 14:26:17: #2 number of paired peaks: 105 WARNING @ Wed, 08 Dec 2021 14:26:17: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Wed, 08 Dec 2021 14:26:17: start model_add_line... INFO @ Wed, 08 Dec 2021 14:26:18: start X-correlation... INFO @ Wed, 08 Dec 2021 14:26:18: end of X-cor INFO @ Wed, 08 Dec 2021 14:26:18: #2 finished! INFO @ Wed, 08 Dec 2021 14:26:18: #2 predicted fragment length is 51 bps INFO @ Wed, 08 Dec 2021 14:26:18: #2 alternative fragment length(s) may be 51,555,568,598 bps INFO @ Wed, 08 Dec 2021 14:26:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.10_model.r WARNING @ Wed, 08 Dec 2021 14:26:18: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:26:18: #2 You may need to consider one of the other alternative d(s): 51,555,568,598 WARNING @ Wed, 08 Dec 2021 14:26:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:26:18: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:26:18: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:26:23: 14000000 INFO @ Wed, 08 Dec 2021 14:26:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:26:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:26:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.05_summits.bed INFO @ Wed, 08 Dec 2021 14:26:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (593 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:26:29: 15000000 INFO @ Wed, 08 Dec 2021 14:26:36: 16000000 INFO @ Wed, 08 Dec 2021 14:26:42: 17000000 INFO @ Wed, 08 Dec 2021 14:26:46: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:26:46: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 14:26:46: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 14:26:46: #1 total tags in treatment: 17660735 INFO @ Wed, 08 Dec 2021 14:26:46: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:26:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 14:26:46: #1 tags after filtering in treatment: 17660735 INFO @ Wed, 08 Dec 2021 14:26:46: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 14:26:46: #1 finished! INFO @ Wed, 08 Dec 2021 14:26:46: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:26:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:26:47: #2 number of paired peaks: 105 WARNING @ Wed, 08 Dec 2021 14:26:47: Fewer paired peaks (105) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 105 pairs to build model! INFO @ Wed, 08 Dec 2021 14:26:47: start model_add_line... INFO @ Wed, 08 Dec 2021 14:26:47: start X-correlation... INFO @ Wed, 08 Dec 2021 14:26:47: end of X-cor INFO @ Wed, 08 Dec 2021 14:26:47: #2 finished! INFO @ Wed, 08 Dec 2021 14:26:47: #2 predicted fragment length is 51 bps INFO @ Wed, 08 Dec 2021 14:26:47: #2 alternative fragment length(s) may be 51,555,568,598 bps INFO @ Wed, 08 Dec 2021 14:26:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.20_model.r WARNING @ Wed, 08 Dec 2021 14:26:47: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:26:47: #2 You may need to consider one of the other alternative d(s): 51,555,568,598 WARNING @ Wed, 08 Dec 2021 14:26:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:26:47: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:26:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:27:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:27:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:27:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.10_summits.bed INFO @ Wed, 08 Dec 2021 14:27:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (317 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:27:15: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:27:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:27:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:27:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10040009/SRX10040009.20_summits.bed INFO @ Wed, 08 Dec 2021 14:27:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (91 records, 4 fields): 1 millis CompletedMACS2peakCalling