Job ID = 16434854 SRX = SRX10435523 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17374353 spots for SRR14060923/SRR14060923.sra Written 17374353 spots for SRR14060923/SRR14060923.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434902 ("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: 00:06:06 17374353 reads; of these: 17374353 (100.00%) were unpaired; of these: 2067834 (11.90%) aligned 0 times 13012122 (74.89%) aligned exactly 1 time 2294397 (13.21%) aligned >1 times 88.10% overall alignment rate Time searching: 00:06:06 Overall time: 00:06:06 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] 2077730 / 15306519 = 0.1357 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 10:14:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.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 10:14:32: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:14:32: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:14:40: 1000000 INFO @ Tue, 02 Aug 2022 10:14:47: 2000000 INFO @ Tue, 02 Aug 2022 10:14:55: 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 10:15:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.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 10:15:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:15:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:15:03: 4000000 INFO @ Tue, 02 Aug 2022 10:15:09: 1000000 INFO @ Tue, 02 Aug 2022 10:15:11: 5000000 INFO @ Tue, 02 Aug 2022 10:15:16: 2000000 INFO @ Tue, 02 Aug 2022 10:15:19: 6000000 INFO @ Tue, 02 Aug 2022 10:15:24: 3000000 INFO @ Tue, 02 Aug 2022 10:15:26: 7000000 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 10:15:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.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 10:15:31: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:15:31: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:15:32: 4000000 INFO @ Tue, 02 Aug 2022 10:15:35: 8000000 INFO @ Tue, 02 Aug 2022 10:15:39: 1000000 INFO @ Tue, 02 Aug 2022 10:15:41: 5000000 INFO @ Tue, 02 Aug 2022 10:15:43: 9000000 INFO @ Tue, 02 Aug 2022 10:15:47: 2000000 INFO @ Tue, 02 Aug 2022 10:15:49: 6000000 INFO @ Tue, 02 Aug 2022 10:15:52: 10000000 INFO @ Tue, 02 Aug 2022 10:15:55: 3000000 INFO @ Tue, 02 Aug 2022 10:15:56: 7000000 INFO @ Tue, 02 Aug 2022 10:16:01: 11000000 INFO @ Tue, 02 Aug 2022 10:16:03: 4000000 INFO @ Tue, 02 Aug 2022 10:16:05: 8000000 INFO @ Tue, 02 Aug 2022 10:16:09: 12000000 INFO @ Tue, 02 Aug 2022 10:16:12: 5000000 INFO @ Tue, 02 Aug 2022 10:16:13: 9000000 INFO @ Tue, 02 Aug 2022 10:16:18: 13000000 INFO @ Tue, 02 Aug 2022 10:16:19: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:16:19: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:16:19: #1 total tags in treatment: 13228789 INFO @ Tue, 02 Aug 2022 10:16:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:16:19: #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 10:16:20: #1 tags after filtering in treatment: 13228789 INFO @ Tue, 02 Aug 2022 10:16:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:16:20: #1 finished! INFO @ Tue, 02 Aug 2022 10:16:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:16:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:16:20: 6000000 INFO @ Tue, 02 Aug 2022 10:16:21: #2 number of paired peaks: 451 WARNING @ Tue, 02 Aug 2022 10:16:21: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Tue, 02 Aug 2022 10:16:21: start model_add_line... INFO @ Tue, 02 Aug 2022 10:16:21: start X-correlation... INFO @ Tue, 02 Aug 2022 10:16:21: end of X-cor INFO @ Tue, 02 Aug 2022 10:16:21: #2 finished! INFO @ Tue, 02 Aug 2022 10:16:21: #2 predicted fragment length is 134 bps INFO @ Tue, 02 Aug 2022 10:16:21: #2 alternative fragment length(s) may be 134 bps INFO @ Tue, 02 Aug 2022 10:16:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.05_model.r WARNING @ Tue, 02 Aug 2022 10:16:21: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:16:21: #2 You may need to consider one of the other alternative d(s): 134 WARNING @ Tue, 02 Aug 2022 10:16:21: #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 10:16:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:16:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:16:21: 10000000 INFO @ Tue, 02 Aug 2022 10:16:28: 7000000 INFO @ Tue, 02 Aug 2022 10:16:29: 11000000 INFO @ Tue, 02 Aug 2022 10:16:36: 8000000 INFO @ Tue, 02 Aug 2022 10:16:38: 12000000 INFO @ Tue, 02 Aug 2022 10:16:44: 9000000 INFO @ Tue, 02 Aug 2022 10:16:47: 13000000 INFO @ Tue, 02 Aug 2022 10:16:48: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:16:49: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:16:49: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:16:49: #1 total tags in treatment: 13228789 INFO @ Tue, 02 Aug 2022 10:16:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:16:49: #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 10:16:49: #1 tags after filtering in treatment: 13228789 INFO @ Tue, 02 Aug 2022 10:16:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:16:49: #1 finished! INFO @ Tue, 02 Aug 2022 10:16:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:16:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:16:50: #2 number of paired peaks: 451 WARNING @ Tue, 02 Aug 2022 10:16:50: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Tue, 02 Aug 2022 10:16:50: start model_add_line... INFO @ Tue, 02 Aug 2022 10:16:51: start X-correlation... INFO @ Tue, 02 Aug 2022 10:16:51: end of X-cor INFO @ Tue, 02 Aug 2022 10:16:51: #2 finished! INFO @ Tue, 02 Aug 2022 10:16:51: #2 predicted fragment length is 134 bps INFO @ Tue, 02 Aug 2022 10:16:51: #2 alternative fragment length(s) may be 134 bps INFO @ Tue, 02 Aug 2022 10:16:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.10_model.r WARNING @ Tue, 02 Aug 2022 10:16:51: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:16:51: #2 You may need to consider one of the other alternative d(s): 134 WARNING @ Tue, 02 Aug 2022 10:16:51: #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 10:16:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:16:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:16:53: 10000000 INFO @ Tue, 02 Aug 2022 10:17:01: 11000000 INFO @ Tue, 02 Aug 2022 10:17:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:17:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:17:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.05_summits.bed INFO @ Tue, 02 Aug 2022 10:17:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2098 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:17:08: 12000000 INFO @ Tue, 02 Aug 2022 10:17:16: 13000000 INFO @ Tue, 02 Aug 2022 10:17:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:17:18: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:17:18: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:17:18: #1 total tags in treatment: 13228789 INFO @ Tue, 02 Aug 2022 10:17:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:17:18: #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 10:17:18: #1 tags after filtering in treatment: 13228789 INFO @ Tue, 02 Aug 2022 10:17:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:17:18: #1 finished! INFO @ Tue, 02 Aug 2022 10:17:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:17:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:17:19: #2 number of paired peaks: 451 WARNING @ Tue, 02 Aug 2022 10:17:19: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Tue, 02 Aug 2022 10:17:19: start model_add_line... INFO @ Tue, 02 Aug 2022 10:17:19: start X-correlation... INFO @ Tue, 02 Aug 2022 10:17:19: end of X-cor INFO @ Tue, 02 Aug 2022 10:17:19: #2 finished! INFO @ Tue, 02 Aug 2022 10:17:19: #2 predicted fragment length is 134 bps INFO @ Tue, 02 Aug 2022 10:17:19: #2 alternative fragment length(s) may be 134 bps INFO @ Tue, 02 Aug 2022 10:17:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.20_model.r WARNING @ Tue, 02 Aug 2022 10:17:19: #2 Since the d (134) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:17:19: #2 You may need to consider one of the other alternative d(s): 134 WARNING @ Tue, 02 Aug 2022 10:17:19: #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 10:17:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:17:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:17:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:17:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:17:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.10_summits.bed INFO @ Tue, 02 Aug 2022 10:17:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1377 records, 4 fields): 83 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:17:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:17:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:17:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:17:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435523/SRX10435523.20_summits.bed INFO @ Tue, 02 Aug 2022 10:17:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (839 records, 4 fields): 42 millis CompletedMACS2peakCalling BigWig に変換しました。