Job ID = 16434897 SRX = SRX11633390 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 22665333 spots for SRR15329098/SRR15329098.sra Written 22665333 spots for SRR15329098/SRR15329098.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434982 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:26 22665333 reads; of these: 22665333 (100.00%) were unpaired; of these: 2155253 (9.51%) aligned 0 times 17645126 (77.85%) aligned exactly 1 time 2864954 (12.64%) aligned >1 times 90.49% overall alignment rate Time searching: 00:07:26 Overall time: 00:07:26 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] 1778079 / 20510080 = 0.0867 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 10:30:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.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 10:30:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:30:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:30:41: 1000000 INFO @ Tue, 02 Aug 2022 10:30:46: 2000000 INFO @ Tue, 02 Aug 2022 10:30:52: 3000000 INFO @ Tue, 02 Aug 2022 10:30:58: 4000000 INFO @ Tue, 02 Aug 2022 10:31:03: 5000000 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 10:31:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.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 10:31:05: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:31:05: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:31:09: 6000000 INFO @ Tue, 02 Aug 2022 10:31:11: 1000000 INFO @ Tue, 02 Aug 2022 10:31:14: 7000000 INFO @ Tue, 02 Aug 2022 10:31:16: 2000000 INFO @ Tue, 02 Aug 2022 10:31:20: 8000000 INFO @ Tue, 02 Aug 2022 10:31:22: 3000000 INFO @ Tue, 02 Aug 2022 10:31:25: 9000000 INFO @ Tue, 02 Aug 2022 10:31:28: 4000000 INFO @ Tue, 02 Aug 2022 10:31:31: 10000000 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 10:31:33: 5000000 INFO @ Tue, 02 Aug 2022 10:31:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.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 10:31:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:31:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:31:36: 11000000 INFO @ Tue, 02 Aug 2022 10:31:39: 6000000 INFO @ Tue, 02 Aug 2022 10:31:41: 1000000 INFO @ Tue, 02 Aug 2022 10:31:41: 12000000 INFO @ Tue, 02 Aug 2022 10:31:45: 7000000 INFO @ Tue, 02 Aug 2022 10:31:47: 13000000 INFO @ Tue, 02 Aug 2022 10:31:47: 2000000 INFO @ Tue, 02 Aug 2022 10:31:50: 8000000 INFO @ Tue, 02 Aug 2022 10:31:52: 14000000 INFO @ Tue, 02 Aug 2022 10:31:53: 3000000 INFO @ Tue, 02 Aug 2022 10:31:56: 9000000 INFO @ Tue, 02 Aug 2022 10:31:58: 15000000 INFO @ Tue, 02 Aug 2022 10:31:59: 4000000 INFO @ Tue, 02 Aug 2022 10:32:01: 10000000 INFO @ Tue, 02 Aug 2022 10:32:03: 16000000 INFO @ Tue, 02 Aug 2022 10:32:05: 5000000 INFO @ Tue, 02 Aug 2022 10:32:07: 11000000 INFO @ Tue, 02 Aug 2022 10:32:09: 17000000 INFO @ Tue, 02 Aug 2022 10:32:11: 6000000 INFO @ Tue, 02 Aug 2022 10:32:12: 12000000 INFO @ Tue, 02 Aug 2022 10:32:14: 18000000 INFO @ Tue, 02 Aug 2022 10:32:17: 7000000 INFO @ Tue, 02 Aug 2022 10:32:18: 13000000 INFO @ Tue, 02 Aug 2022 10:32:18: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:32:18: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:32:18: #1 total tags in treatment: 18732001 INFO @ Tue, 02 Aug 2022 10:32:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:32:18: #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 10:32:19: #1 tags after filtering in treatment: 18732001 INFO @ Tue, 02 Aug 2022 10:32:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:32:19: #1 finished! INFO @ Tue, 02 Aug 2022 10:32:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:32:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:32:20: #2 number of paired peaks: 145 WARNING @ Tue, 02 Aug 2022 10:32:20: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Tue, 02 Aug 2022 10:32:20: start model_add_line... INFO @ Tue, 02 Aug 2022 10:32:20: start X-correlation... INFO @ Tue, 02 Aug 2022 10:32:20: end of X-cor INFO @ Tue, 02 Aug 2022 10:32:20: #2 finished! INFO @ Tue, 02 Aug 2022 10:32:20: #2 predicted fragment length is 62 bps INFO @ Tue, 02 Aug 2022 10:32:20: #2 alternative fragment length(s) may be 2,62,545 bps INFO @ Tue, 02 Aug 2022 10:32:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.05_model.r WARNING @ Tue, 02 Aug 2022 10:32:20: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:32:20: #2 You may need to consider one of the other alternative d(s): 2,62,545 WARNING @ Tue, 02 Aug 2022 10:32:20: #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 10:32:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:32:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:32:23: 8000000 INFO @ Tue, 02 Aug 2022 10:32:23: 14000000 INFO @ Tue, 02 Aug 2022 10:32:28: 15000000 INFO @ Tue, 02 Aug 2022 10:32:29: 9000000 INFO @ Tue, 02 Aug 2022 10:32:34: 16000000 INFO @ Tue, 02 Aug 2022 10:32:35: 10000000 INFO @ Tue, 02 Aug 2022 10:32:40: 17000000 INFO @ Tue, 02 Aug 2022 10:32:41: 11000000 INFO @ Tue, 02 Aug 2022 10:32:45: 18000000 INFO @ Tue, 02 Aug 2022 10:32:48: 12000000 INFO @ Tue, 02 Aug 2022 10:32:50: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:32:50: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:32:50: #1 total tags in treatment: 18732001 INFO @ Tue, 02 Aug 2022 10:32:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:32:50: #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 10:32:50: #1 tags after filtering in treatment: 18732001 INFO @ Tue, 02 Aug 2022 10:32:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:32:50: #1 finished! INFO @ Tue, 02 Aug 2022 10:32:50: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:32:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:32:51: #2 number of paired peaks: 145 WARNING @ Tue, 02 Aug 2022 10:32:51: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Tue, 02 Aug 2022 10:32:51: start model_add_line... INFO @ Tue, 02 Aug 2022 10:32:51: start X-correlation... INFO @ Tue, 02 Aug 2022 10:32:51: end of X-cor INFO @ Tue, 02 Aug 2022 10:32:51: #2 finished! INFO @ Tue, 02 Aug 2022 10:32:51: #2 predicted fragment length is 62 bps INFO @ Tue, 02 Aug 2022 10:32:51: #2 alternative fragment length(s) may be 2,62,545 bps INFO @ Tue, 02 Aug 2022 10:32:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.10_model.r WARNING @ Tue, 02 Aug 2022 10:32:51: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:32:51: #2 You may need to consider one of the other alternative d(s): 2,62,545 WARNING @ Tue, 02 Aug 2022 10:32:51: #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 10:32:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:32:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:32:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:32:53: 13000000 INFO @ Tue, 02 Aug 2022 10:33:00: 14000000 INFO @ Tue, 02 Aug 2022 10:33:06: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:33:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:33:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:33:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.05_summits.bed INFO @ Tue, 02 Aug 2022 10:33:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (540 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:33:12: 16000000 INFO @ Tue, 02 Aug 2022 10:33:18: 17000000 INFO @ Tue, 02 Aug 2022 10:33:24: 18000000 INFO @ Tue, 02 Aug 2022 10:33:24: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:33:28: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 10:33:28: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 10:33:28: #1 total tags in treatment: 18732001 INFO @ Tue, 02 Aug 2022 10:33:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:33:28: #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 10:33:29: #1 tags after filtering in treatment: 18732001 INFO @ Tue, 02 Aug 2022 10:33:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:33:29: #1 finished! INFO @ Tue, 02 Aug 2022 10:33:29: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:33:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:33:30: #2 number of paired peaks: 145 WARNING @ Tue, 02 Aug 2022 10:33:30: Fewer paired peaks (145) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 145 pairs to build model! INFO @ Tue, 02 Aug 2022 10:33:30: start model_add_line... INFO @ Tue, 02 Aug 2022 10:33:30: start X-correlation... INFO @ Tue, 02 Aug 2022 10:33:30: end of X-cor INFO @ Tue, 02 Aug 2022 10:33:30: #2 finished! INFO @ Tue, 02 Aug 2022 10:33:30: #2 predicted fragment length is 62 bps INFO @ Tue, 02 Aug 2022 10:33:30: #2 alternative fragment length(s) may be 2,62,545 bps INFO @ Tue, 02 Aug 2022 10:33:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.20_model.r WARNING @ Tue, 02 Aug 2022 10:33:30: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:33:30: #2 You may need to consider one of the other alternative d(s): 2,62,545 WARNING @ Tue, 02 Aug 2022 10:33:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 10:33:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:33:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:33:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:33:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:33:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.10_summits.bed INFO @ Tue, 02 Aug 2022 10:33:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (340 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:34:01: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:34:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:34:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:34:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX11633390/SRX11633390.20_summits.bed INFO @ Tue, 02 Aug 2022 10:34:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (174 records, 4 fields): 1 millis CompletedMACS2peakCalling