Job ID = 16434791 SRX = SRX10925685 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21552988 spots for SRR14580053/SRR14580053.sra Written 21552988 spots for SRR14580053/SRR14580053.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434872 ("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: 00:06:52 21552988 reads; of these: 21552988 (100.00%) were unpaired; of these: 5136259 (23.83%) aligned 0 times 13530846 (62.78%) aligned exactly 1 time 2885883 (13.39%) aligned >1 times 76.17% overall alignment rate Time searching: 00:06:52 Overall time: 00:06:52 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] 2475635 / 16416729 = 0.1508 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 10:08:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.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 10:08:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:08:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:09:05: 1000000 INFO @ Tue, 02 Aug 2022 10:09:12: 2000000 INFO @ Tue, 02 Aug 2022 10:09:19: 3000000 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 10:09:26: 4000000 INFO @ Tue, 02 Aug 2022 10:09:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.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 10:09:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:09:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:09:34: 5000000 INFO @ Tue, 02 Aug 2022 10:09:35: 1000000 INFO @ Tue, 02 Aug 2022 10:09:42: 6000000 INFO @ Tue, 02 Aug 2022 10:09:43: 2000000 INFO @ Tue, 02 Aug 2022 10:09:50: 7000000 INFO @ Tue, 02 Aug 2022 10:09:51: 3000000 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 10:09:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.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 10:09:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:09:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:09:58: 8000000 INFO @ Tue, 02 Aug 2022 10:09:59: 4000000 INFO @ Tue, 02 Aug 2022 10:10:06: 1000000 INFO @ Tue, 02 Aug 2022 10:10:06: 9000000 INFO @ Tue, 02 Aug 2022 10:10:07: 5000000 INFO @ Tue, 02 Aug 2022 10:10:14: 2000000 INFO @ Tue, 02 Aug 2022 10:10:14: 10000000 INFO @ Tue, 02 Aug 2022 10:10:15: 6000000 INFO @ Tue, 02 Aug 2022 10:10:22: 3000000 INFO @ Tue, 02 Aug 2022 10:10:23: 11000000 INFO @ Tue, 02 Aug 2022 10:10:23: 7000000 INFO @ Tue, 02 Aug 2022 10:10:30: 4000000 INFO @ Tue, 02 Aug 2022 10:10:31: 12000000 INFO @ Tue, 02 Aug 2022 10:10:31: 8000000 INFO @ Tue, 02 Aug 2022 10:10:39: 5000000 INFO @ Tue, 02 Aug 2022 10:10:39: 13000000 INFO @ Tue, 02 Aug 2022 10:10:39: 9000000 INFO @ Tue, 02 Aug 2022 10:10:47: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:10:47: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:10:47: #1 total tags in treatment: 13941094 INFO @ Tue, 02 Aug 2022 10:10:47: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:10:47: #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 10:10:47: #1 tags after filtering in treatment: 13941094 INFO @ Tue, 02 Aug 2022 10:10:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:10:47: #1 finished! INFO @ Tue, 02 Aug 2022 10:10:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:10:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:10:47: 6000000 INFO @ Tue, 02 Aug 2022 10:10:47: 10000000 INFO @ Tue, 02 Aug 2022 10:10:48: #2 number of paired peaks: 219 WARNING @ Tue, 02 Aug 2022 10:10:48: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Tue, 02 Aug 2022 10:10:48: start model_add_line... INFO @ Tue, 02 Aug 2022 10:10:48: start X-correlation... INFO @ Tue, 02 Aug 2022 10:10:48: end of X-cor INFO @ Tue, 02 Aug 2022 10:10:48: #2 finished! INFO @ Tue, 02 Aug 2022 10:10:48: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 10:10:48: #2 alternative fragment length(s) may be 3,72 bps INFO @ Tue, 02 Aug 2022 10:10:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.05_model.r WARNING @ Tue, 02 Aug 2022 10:10:48: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:10:48: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Tue, 02 Aug 2022 10:10:48: #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 10:10:48: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:10:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:10:55: 11000000 INFO @ Tue, 02 Aug 2022 10:10:55: 7000000 INFO @ Tue, 02 Aug 2022 10:11:03: 12000000 INFO @ Tue, 02 Aug 2022 10:11:03: 8000000 INFO @ Tue, 02 Aug 2022 10:11:11: 13000000 INFO @ Tue, 02 Aug 2022 10:11:11: 9000000 INFO @ Tue, 02 Aug 2022 10:11:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:11:18: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:11:18: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:11:18: #1 total tags in treatment: 13941094 INFO @ Tue, 02 Aug 2022 10:11:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:11:18: #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 10:11:18: #1 tags after filtering in treatment: 13941094 INFO @ Tue, 02 Aug 2022 10:11:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:11:18: #1 finished! INFO @ Tue, 02 Aug 2022 10:11:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:11:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:11:19: 10000000 INFO @ Tue, 02 Aug 2022 10:11:19: #2 number of paired peaks: 219 WARNING @ Tue, 02 Aug 2022 10:11:19: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Tue, 02 Aug 2022 10:11:19: start model_add_line... INFO @ Tue, 02 Aug 2022 10:11:19: start X-correlation... INFO @ Tue, 02 Aug 2022 10:11:19: end of X-cor INFO @ Tue, 02 Aug 2022 10:11:19: #2 finished! INFO @ Tue, 02 Aug 2022 10:11:19: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 10:11:19: #2 alternative fragment length(s) may be 3,72 bps INFO @ Tue, 02 Aug 2022 10:11:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.10_model.r WARNING @ Tue, 02 Aug 2022 10:11:20: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:11:20: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Tue, 02 Aug 2022 10:11:20: #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 10:11:20: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:11:20: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:11:26: 11000000 INFO @ Tue, 02 Aug 2022 10:11:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:11:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:11:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.05_summits.bed INFO @ Tue, 02 Aug 2022 10:11:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (599 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:11:34: 12000000 INFO @ Tue, 02 Aug 2022 10:11:41: 13000000 INFO @ Tue, 02 Aug 2022 10:11:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:11:48: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 10:11:48: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 10:11:48: #1 total tags in treatment: 13941094 INFO @ Tue, 02 Aug 2022 10:11:48: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:11:48: #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 10:11:48: #1 tags after filtering in treatment: 13941094 INFO @ Tue, 02 Aug 2022 10:11:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:11:48: #1 finished! INFO @ Tue, 02 Aug 2022 10:11:48: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:11:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:11:49: #2 number of paired peaks: 219 WARNING @ Tue, 02 Aug 2022 10:11:49: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Tue, 02 Aug 2022 10:11:49: start model_add_line... INFO @ Tue, 02 Aug 2022 10:11:49: start X-correlation... INFO @ Tue, 02 Aug 2022 10:11:50: end of X-cor INFO @ Tue, 02 Aug 2022 10:11:50: #2 finished! INFO @ Tue, 02 Aug 2022 10:11:50: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 10:11:50: #2 alternative fragment length(s) may be 3,72 bps INFO @ Tue, 02 Aug 2022 10:11:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.20_model.r WARNING @ Tue, 02 Aug 2022 10:11:50: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:11:50: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Tue, 02 Aug 2022 10:11:50: #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 10:11:50: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:11:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:11:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:11:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:11:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.10_summits.bed INFO @ Tue, 02 Aug 2022 10:11:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (323 records, 4 fields): 40 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:12:15: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:12:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:12:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:12:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10925685/SRX10925685.20_summits.bed INFO @ Tue, 02 Aug 2022 10:12:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 1 millis CompletedMACS2peakCalling