Job ID = 14157881 SRX = SRX10040012 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 22508207 spots for SRR13642809/SRR13642809.sra Written 22508207 spots for SRR13642809/SRR13642809.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158083 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:14 22508207 reads; of these: 22508207 (100.00%) were unpaired; of these: 1513461 (6.72%) aligned 0 times 16001280 (71.09%) aligned exactly 1 time 4993466 (22.19%) aligned >1 times 93.28% overall alignment rate Time searching: 00:05:15 Overall time: 00:05:15 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] 3273961 / 20994746 = 0.1559 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 12:32:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.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 12:32:05: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:32:05: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:32:10: 1000000 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 12:32:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.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 12:32:13: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:32:13: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:32:15: 2000000 INFO @ Wed, 08 Dec 2021 12:32:18: 1000000 INFO @ Wed, 08 Dec 2021 12:32:20: 3000000 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 12:32:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.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 12:32:23: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:32:23: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:32:23: 2000000 INFO @ Wed, 08 Dec 2021 12:32:25: 4000000 INFO @ Wed, 08 Dec 2021 12:32:28: 1000000 INFO @ Wed, 08 Dec 2021 12:32:28: 3000000 INFO @ Wed, 08 Dec 2021 12:32:30: 5000000 INFO @ Wed, 08 Dec 2021 12:32:33: 2000000 INFO @ Wed, 08 Dec 2021 12:32:33: 4000000 INFO @ Wed, 08 Dec 2021 12:32:35: 6000000 INFO @ Wed, 08 Dec 2021 12:32:37: 3000000 INFO @ Wed, 08 Dec 2021 12:32:38: 5000000 INFO @ Wed, 08 Dec 2021 12:32:40: 7000000 INFO @ Wed, 08 Dec 2021 12:32:42: 4000000 INFO @ Wed, 08 Dec 2021 12:32:42: 6000000 INFO @ Wed, 08 Dec 2021 12:32:44: 8000000 INFO @ Wed, 08 Dec 2021 12:32:46: 5000000 INFO @ Wed, 08 Dec 2021 12:32:47: 7000000 INFO @ Wed, 08 Dec 2021 12:32:49: 9000000 INFO @ Wed, 08 Dec 2021 12:32:51: 6000000 INFO @ Wed, 08 Dec 2021 12:32:52: 8000000 INFO @ Wed, 08 Dec 2021 12:32:54: 10000000 INFO @ Wed, 08 Dec 2021 12:32:56: 7000000 INFO @ Wed, 08 Dec 2021 12:32:57: 9000000 INFO @ Wed, 08 Dec 2021 12:32:59: 11000000 INFO @ Wed, 08 Dec 2021 12:33:00: 8000000 INFO @ Wed, 08 Dec 2021 12:33:02: 10000000 INFO @ Wed, 08 Dec 2021 12:33:04: 12000000 INFO @ Wed, 08 Dec 2021 12:33:05: 9000000 INFO @ Wed, 08 Dec 2021 12:33:07: 11000000 INFO @ Wed, 08 Dec 2021 12:33:09: 10000000 INFO @ Wed, 08 Dec 2021 12:33:09: 13000000 INFO @ Wed, 08 Dec 2021 12:33:12: 12000000 INFO @ Wed, 08 Dec 2021 12:33:14: 11000000 INFO @ Wed, 08 Dec 2021 12:33:15: 14000000 INFO @ Wed, 08 Dec 2021 12:33:17: 13000000 INFO @ Wed, 08 Dec 2021 12:33:19: 12000000 INFO @ Wed, 08 Dec 2021 12:33:20: 15000000 INFO @ Wed, 08 Dec 2021 12:33:22: 14000000 INFO @ Wed, 08 Dec 2021 12:33:23: 13000000 INFO @ Wed, 08 Dec 2021 12:33:26: 16000000 INFO @ Wed, 08 Dec 2021 12:33:27: 15000000 INFO @ Wed, 08 Dec 2021 12:33:28: 14000000 INFO @ Wed, 08 Dec 2021 12:33:31: 17000000 INFO @ Wed, 08 Dec 2021 12:33:33: 16000000 INFO @ Wed, 08 Dec 2021 12:33:34: 15000000 INFO @ Wed, 08 Dec 2021 12:33:35: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 12:33:35: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 12:33:35: #1 total tags in treatment: 17720785 INFO @ Wed, 08 Dec 2021 12:33:35: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:33:35: #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 12:33:35: #1 tags after filtering in treatment: 17720785 INFO @ Wed, 08 Dec 2021 12:33:35: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:33:35: #1 finished! INFO @ Wed, 08 Dec 2021 12:33:35: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:33:35: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 INFO @ Wed, 08 Dec 2021 12:33:37: #2 number of paired peaks: 346 WARNING @ Wed, 08 Dec 2021 12:33:37: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Wed, 08 Dec 2021 12:33:37: start model_add_line... INFO @ Wed, 08 Dec 2021 12:33:37: start X-correlation... INFO @ Wed, 08 Dec 2021 12:33:37: end of X-cor INFO @ Wed, 08 Dec 2021 12:33:37: #2 finished! INFO @ Wed, 08 Dec 2021 12:33:37: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 12:33:37: #2 alternative fragment length(s) may be 1,38,47 bps INFO @ Wed, 08 Dec 2021 12:33:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.05_model.r WARNING @ Wed, 08 Dec 2021 12:33:37: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:33:37: #2 You may need to consider one of the other alternative d(s): 1,38,47 WARNING @ Wed, 08 Dec 2021 12:33:37: #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 12:33:37: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:33:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換中... INFO @ Wed, 08 Dec 2021 12:33:38: 17000000 INFO @ Wed, 08 Dec 2021 12:33:39: 16000000 INFO @ Wed, 08 Dec 2021 12:33:42: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 12:33:42: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 12:33:42: #1 total tags in treatment: 17720785 INFO @ Wed, 08 Dec 2021 12:33:42: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:33:42: #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 12:33:42: #1 tags after filtering in treatment: 17720785 INFO @ Wed, 08 Dec 2021 12:33:42: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:33:42: #1 finished! INFO @ Wed, 08 Dec 2021 12:33:42: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:33:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:33:44: #2 number of paired peaks: 346 WARNING @ Wed, 08 Dec 2021 12:33:44: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Wed, 08 Dec 2021 12:33:44: start model_add_line... INFO @ Wed, 08 Dec 2021 12:33:44: start X-correlation... INFO @ Wed, 08 Dec 2021 12:33:44: end of X-cor INFO @ Wed, 08 Dec 2021 12:33:44: #2 finished! INFO @ Wed, 08 Dec 2021 12:33:44: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 12:33:44: #2 alternative fragment length(s) may be 1,38,47 bps INFO @ Wed, 08 Dec 2021 12:33:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.10_model.r WARNING @ Wed, 08 Dec 2021 12:33:44: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:33:44: #2 You may need to consider one of the other alternative d(s): 1,38,47 WARNING @ Wed, 08 Dec 2021 12:33:44: #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 12:33:44: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:33:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:33:44: 17000000 INFO @ Wed, 08 Dec 2021 12:33:48: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 12:33:48: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 12:33:48: #1 total tags in treatment: 17720785 INFO @ Wed, 08 Dec 2021 12:33:48: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:33:48: #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 12:33:48: #1 tags after filtering in treatment: 17720785 INFO @ Wed, 08 Dec 2021 12:33:48: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:33:48: #1 finished! INFO @ Wed, 08 Dec 2021 12:33:48: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:33:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:33:49: #2 number of paired peaks: 346 WARNING @ Wed, 08 Dec 2021 12:33:49: Fewer paired peaks (346) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 346 pairs to build model! INFO @ Wed, 08 Dec 2021 12:33:49: start model_add_line... INFO @ Wed, 08 Dec 2021 12:33:49: start X-correlation... INFO @ Wed, 08 Dec 2021 12:33:50: end of X-cor INFO @ Wed, 08 Dec 2021 12:33:50: #2 finished! INFO @ Wed, 08 Dec 2021 12:33:50: #2 predicted fragment length is 47 bps INFO @ Wed, 08 Dec 2021 12:33:50: #2 alternative fragment length(s) may be 1,38,47 bps INFO @ Wed, 08 Dec 2021 12:33:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.20_model.r WARNING @ Wed, 08 Dec 2021 12:33:50: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:33:50: #2 You may need to consider one of the other alternative d(s): 1,38,47 WARNING @ Wed, 08 Dec 2021 12:33:50: #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 12:33:50: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:33:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:34:08: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:34:15: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:34:20: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:34:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.05_peaks.xls INFO @ Wed, 08 Dec 2021 12:34:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:34:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.05_summits.bed INFO @ Wed, 08 Dec 2021 12:34:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1204 records, 4 fields): 2 millis INFO @ Wed, 08 Dec 2021 12:34:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.10_peaks.xls INFO @ Wed, 08 Dec 2021 12:34:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:34:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.10_summits.bed INFO @ Wed, 08 Dec 2021 12:34:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (446 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 12:34:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.20_peaks.xls INFO @ Wed, 08 Dec 2021 12:34:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:34:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10040012/SRX10040012.20_summits.bed INFO @ Wed, 08 Dec 2021 12:34:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (154 records, 4 fields): 1 millis CompletedMACS2peakCalling