Job ID = 16434122 SRX = SRX10274853 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: 00:08:16 21556302 reads; of these: 21556302 (100.00%) were unpaired; of these: 592729 (2.75%) aligned 0 times 17360822 (80.54%) aligned exactly 1 time 3602751 (16.71%) aligned >1 times 97.25% overall alignment rate Time searching: 00:08:16 Overall time: 00:08:16 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] 3875172 / 20963573 = 0.1849 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:00:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.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, 02 Aug 2022 10:00:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:00:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:00:36: 1000000 INFO @ Tue, 02 Aug 2022 10:00:43: 2000000 INFO @ Tue, 02 Aug 2022 10:00:49: 3000000 INFO @ Tue, 02 Aug 2022 10:00:55: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:00:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.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, 02 Aug 2022 10:00:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:00:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:01:02: 5000000 INFO @ Tue, 02 Aug 2022 10:01:06: 1000000 INFO @ Tue, 02 Aug 2022 10:01:09: 6000000 INFO @ Tue, 02 Aug 2022 10:01:14: 2000000 INFO @ Tue, 02 Aug 2022 10:01:17: 7000000 INFO @ Tue, 02 Aug 2022 10:01:21: 3000000 INFO @ Tue, 02 Aug 2022 10:01:24: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 10:01:28: 4000000 INFO @ Tue, 02 Aug 2022 10:01:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.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, 02 Aug 2022 10:01:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:01:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:01:31: 9000000 INFO @ Tue, 02 Aug 2022 10:01:35: 5000000 INFO @ Tue, 02 Aug 2022 10:01:36: 1000000 INFO @ Tue, 02 Aug 2022 10:01:38: 10000000 INFO @ Tue, 02 Aug 2022 10:01:42: 6000000 INFO @ Tue, 02 Aug 2022 10:01:43: 2000000 INFO @ Tue, 02 Aug 2022 10:01:46: 11000000 INFO @ Tue, 02 Aug 2022 10:01:50: 7000000 INFO @ Tue, 02 Aug 2022 10:01:50: 3000000 INFO @ Tue, 02 Aug 2022 10:01:53: 12000000 INFO @ Tue, 02 Aug 2022 10:01:57: 4000000 INFO @ Tue, 02 Aug 2022 10:01:57: 8000000 INFO @ Tue, 02 Aug 2022 10:02:00: 13000000 INFO @ Tue, 02 Aug 2022 10:02:04: 5000000 INFO @ Tue, 02 Aug 2022 10:02:04: 9000000 INFO @ Tue, 02 Aug 2022 10:02:08: 14000000 INFO @ Tue, 02 Aug 2022 10:02:11: 6000000 INFO @ Tue, 02 Aug 2022 10:02:11: 10000000 INFO @ Tue, 02 Aug 2022 10:02:15: 15000000 INFO @ Tue, 02 Aug 2022 10:02:18: 7000000 INFO @ Tue, 02 Aug 2022 10:02:18: 11000000 INFO @ Tue, 02 Aug 2022 10:02:22: 16000000 INFO @ Tue, 02 Aug 2022 10:02:25: 8000000 INFO @ Tue, 02 Aug 2022 10:02:25: 12000000 INFO @ Tue, 02 Aug 2022 10:02:29: 17000000 INFO @ Tue, 02 Aug 2022 10:02:30: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:02:30: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:02:30: #1 total tags in treatment: 17088401 INFO @ Tue, 02 Aug 2022 10:02:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:02:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:02:30: #1 tags after filtering in treatment: 17088401 INFO @ Tue, 02 Aug 2022 10:02:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:02:30: #1 finished! INFO @ Tue, 02 Aug 2022 10:02:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:02:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:02:31: 9000000 INFO @ Tue, 02 Aug 2022 10:02:31: 13000000 INFO @ Tue, 02 Aug 2022 10:02:31: #2 number of paired peaks: 296 WARNING @ Tue, 02 Aug 2022 10:02:31: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Tue, 02 Aug 2022 10:02:31: start model_add_line... INFO @ Tue, 02 Aug 2022 10:02:32: start X-correlation... INFO @ Tue, 02 Aug 2022 10:02:32: end of X-cor INFO @ Tue, 02 Aug 2022 10:02:32: #2 finished! INFO @ Tue, 02 Aug 2022 10:02:32: #2 predicted fragment length is 97 bps INFO @ Tue, 02 Aug 2022 10:02:32: #2 alternative fragment length(s) may be 3,97 bps INFO @ Tue, 02 Aug 2022 10:02:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.05_model.r WARNING @ Tue, 02 Aug 2022 10:02:32: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:02:32: #2 You may need to consider one of the other alternative d(s): 3,97 WARNING @ Tue, 02 Aug 2022 10:02:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:02:32: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:02:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:02:38: 10000000 INFO @ Tue, 02 Aug 2022 10:02:38: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:02:44: 11000000 INFO @ Tue, 02 Aug 2022 10:02:44: 15000000 INFO @ Tue, 02 Aug 2022 10:02:51: 12000000 INFO @ Tue, 02 Aug 2022 10:02:51: 16000000 INFO @ Tue, 02 Aug 2022 10:02:57: 13000000 INFO @ Tue, 02 Aug 2022 10:02:57: 17000000 INFO @ Tue, 02 Aug 2022 10:02:58: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:02:58: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:02:58: #1 total tags in treatment: 17088401 INFO @ Tue, 02 Aug 2022 10:02:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:02:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:02:58: #1 tags after filtering in treatment: 17088401 INFO @ Tue, 02 Aug 2022 10:02:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:02:58: #1 finished! INFO @ Tue, 02 Aug 2022 10:02:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:02:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:02:59: #2 number of paired peaks: 296 WARNING @ Tue, 02 Aug 2022 10:02:59: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Tue, 02 Aug 2022 10:02:59: start model_add_line... INFO @ Tue, 02 Aug 2022 10:02:59: start X-correlation... INFO @ Tue, 02 Aug 2022 10:02:59: end of X-cor INFO @ Tue, 02 Aug 2022 10:02:59: #2 finished! INFO @ Tue, 02 Aug 2022 10:02:59: #2 predicted fragment length is 97 bps INFO @ Tue, 02 Aug 2022 10:02:59: #2 alternative fragment length(s) may be 3,97 bps INFO @ Tue, 02 Aug 2022 10:02:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.10_model.r WARNING @ Tue, 02 Aug 2022 10:03:00: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:03:00: #2 You may need to consider one of the other alternative d(s): 3,97 WARNING @ Tue, 02 Aug 2022 10:03:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:03:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:03:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:03:03: 14000000 INFO @ Tue, 02 Aug 2022 10:03:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:03:09: 15000000 INFO @ Tue, 02 Aug 2022 10:03:14: 16000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:03:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:03:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:03:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.05_summits.bed INFO @ Tue, 02 Aug 2022 10:03:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (8335 records, 4 fields): 51 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:03:20: 17000000 INFO @ Tue, 02 Aug 2022 10:03:21: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:03:21: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:03:21: #1 total tags in treatment: 17088401 INFO @ Tue, 02 Aug 2022 10:03:21: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:03:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 10:03:21: #1 tags after filtering in treatment: 17088401 INFO @ Tue, 02 Aug 2022 10:03:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:03:21: #1 finished! INFO @ Tue, 02 Aug 2022 10:03:21: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:03:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:03:22: #2 number of paired peaks: 296 WARNING @ Tue, 02 Aug 2022 10:03:22: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Tue, 02 Aug 2022 10:03:22: start model_add_line... INFO @ Tue, 02 Aug 2022 10:03:22: start X-correlation... INFO @ Tue, 02 Aug 2022 10:03:22: end of X-cor INFO @ Tue, 02 Aug 2022 10:03:22: #2 finished! INFO @ Tue, 02 Aug 2022 10:03:22: #2 predicted fragment length is 97 bps INFO @ Tue, 02 Aug 2022 10:03:22: #2 alternative fragment length(s) may be 3,97 bps INFO @ Tue, 02 Aug 2022 10:03:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.20_model.r WARNING @ Tue, 02 Aug 2022 10:03:22: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:03:22: #2 You may need to consider one of the other alternative d(s): 3,97 WARNING @ Tue, 02 Aug 2022 10:03:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:03:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:03:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:03:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:03:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:03:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:03:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.10_summits.bed INFO @ Tue, 02 Aug 2022 10:03:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2870 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:03:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:04:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:04:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:04:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10274853/SRX10274853.20_summits.bed INFO @ Tue, 02 Aug 2022 10:04:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (632 records, 4 fields): 13 millis CompletedMACS2peakCalling