Job ID = 14159685 SRX = SRX8832063 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 32508562 spots for SRR12332005/SRR12332005.sra Written 32508562 spots for SRR12332005/SRR12332005.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160301 ("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: 00:08:18 32508562 reads; of these: 32508562 (100.00%) were unpaired; of these: 493168 (1.52%) aligned 0 times 27114447 (83.41%) aligned exactly 1 time 4900947 (15.08%) aligned >1 times 98.48% overall alignment rate Time searching: 00:08:18 Overall time: 00:08:18 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 16 files... [bam_rmdupse_core] 9732707 / 32015394 = 0.3040 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 @ Thu, 09 Dec 2021 00:37:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.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 @ Thu, 09 Dec 2021 00:37:56: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:37:56: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:38:01: 1000000 INFO @ Thu, 09 Dec 2021 00:38:05: 2000000 INFO @ Thu, 09 Dec 2021 00:38:10: 3000000 INFO @ Thu, 09 Dec 2021 00:38:14: 4000000 INFO @ Thu, 09 Dec 2021 00:38:19: 5000000 INFO @ Thu, 09 Dec 2021 00:38:23: 6000000 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 @ Thu, 09 Dec 2021 00:38:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.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 @ Thu, 09 Dec 2021 00:38:26: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:38:26: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:38:28: 7000000 INFO @ Thu, 09 Dec 2021 00:38:31: 1000000 INFO @ Thu, 09 Dec 2021 00:38:33: 8000000 INFO @ Thu, 09 Dec 2021 00:38:36: 2000000 INFO @ Thu, 09 Dec 2021 00:38:38: 9000000 INFO @ Thu, 09 Dec 2021 00:38:40: 3000000 INFO @ Thu, 09 Dec 2021 00:38:42: 10000000 INFO @ Thu, 09 Dec 2021 00:38:45: 4000000 INFO @ Thu, 09 Dec 2021 00:38:47: 11000000 INFO @ Thu, 09 Dec 2021 00:38:50: 5000000 INFO @ Thu, 09 Dec 2021 00:38:52: 12000000 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 @ Thu, 09 Dec 2021 00:38:55: 6000000 INFO @ Thu, 09 Dec 2021 00:38:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.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 @ Thu, 09 Dec 2021 00:38:56: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:38:56: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:38:56: 13000000 INFO @ Thu, 09 Dec 2021 00:39:00: 7000000 INFO @ Thu, 09 Dec 2021 00:39:01: 1000000 INFO @ Thu, 09 Dec 2021 00:39:01: 14000000 INFO @ Thu, 09 Dec 2021 00:39:04: 8000000 INFO @ Thu, 09 Dec 2021 00:39:06: 2000000 INFO @ Thu, 09 Dec 2021 00:39:06: 15000000 INFO @ Thu, 09 Dec 2021 00:39:09: 9000000 INFO @ Thu, 09 Dec 2021 00:39:11: 3000000 INFO @ Thu, 09 Dec 2021 00:39:11: 16000000 INFO @ Thu, 09 Dec 2021 00:39:14: 10000000 INFO @ Thu, 09 Dec 2021 00:39:15: 4000000 INFO @ Thu, 09 Dec 2021 00:39:16: 17000000 INFO @ Thu, 09 Dec 2021 00:39:19: 11000000 INFO @ Thu, 09 Dec 2021 00:39:20: 5000000 INFO @ Thu, 09 Dec 2021 00:39:20: 18000000 INFO @ Thu, 09 Dec 2021 00:39:24: 12000000 INFO @ Thu, 09 Dec 2021 00:39:25: 6000000 INFO @ Thu, 09 Dec 2021 00:39:25: 19000000 INFO @ Thu, 09 Dec 2021 00:39:28: 13000000 INFO @ Thu, 09 Dec 2021 00:39:30: 7000000 INFO @ Thu, 09 Dec 2021 00:39:30: 20000000 INFO @ Thu, 09 Dec 2021 00:39:33: 14000000 INFO @ Thu, 09 Dec 2021 00:39:35: 8000000 INFO @ Thu, 09 Dec 2021 00:39:35: 21000000 INFO @ Thu, 09 Dec 2021 00:39:38: 15000000 INFO @ Thu, 09 Dec 2021 00:39:39: 9000000 INFO @ Thu, 09 Dec 2021 00:39:40: 22000000 INFO @ Thu, 09 Dec 2021 00:39:41: #1 tag size is determined as 49 bps INFO @ Thu, 09 Dec 2021 00:39:41: #1 tag size = 49 INFO @ Thu, 09 Dec 2021 00:39:41: #1 total tags in treatment: 22282687 INFO @ Thu, 09 Dec 2021 00:39:41: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:39:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:39:41: #1 tags after filtering in treatment: 22282687 INFO @ Thu, 09 Dec 2021 00:39:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:39:41: #1 finished! INFO @ Thu, 09 Dec 2021 00:39:41: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:39:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:39:43: #2 number of paired peaks: 118 WARNING @ Thu, 09 Dec 2021 00:39:43: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Thu, 09 Dec 2021 00:39:43: start model_add_line... INFO @ Thu, 09 Dec 2021 00:39:43: 16000000 INFO @ Thu, 09 Dec 2021 00:39:43: start X-correlation... INFO @ Thu, 09 Dec 2021 00:39:43: end of X-cor INFO @ Thu, 09 Dec 2021 00:39:43: #2 finished! INFO @ Thu, 09 Dec 2021 00:39:43: #2 predicted fragment length is 47 bps INFO @ Thu, 09 Dec 2021 00:39:43: #2 alternative fragment length(s) may be 2,47,598 bps INFO @ Thu, 09 Dec 2021 00:39:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.05_model.r WARNING @ Thu, 09 Dec 2021 00:39:43: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:39:43: #2 You may need to consider one of the other alternative d(s): 2,47,598 WARNING @ Thu, 09 Dec 2021 00:39:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 00:39:43: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:39:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:39:44: 10000000 INFO @ Thu, 09 Dec 2021 00:39:48: 17000000 INFO @ Thu, 09 Dec 2021 00:39:49: 11000000 INFO @ Thu, 09 Dec 2021 00:39:52: 18000000 INFO @ Thu, 09 Dec 2021 00:39:54: 12000000 INFO @ Thu, 09 Dec 2021 00:39:57: 19000000 INFO @ Thu, 09 Dec 2021 00:39:58: 13000000 INFO @ Thu, 09 Dec 2021 00:40:02: 20000000 INFO @ Thu, 09 Dec 2021 00:40:03: 14000000 INFO @ Thu, 09 Dec 2021 00:40:07: 21000000 INFO @ Thu, 09 Dec 2021 00:40:08: 15000000 INFO @ Thu, 09 Dec 2021 00:40:11: 22000000 INFO @ Thu, 09 Dec 2021 00:40:13: 16000000 INFO @ Thu, 09 Dec 2021 00:40:13: #1 tag size is determined as 49 bps INFO @ Thu, 09 Dec 2021 00:40:13: #1 tag size = 49 INFO @ Thu, 09 Dec 2021 00:40:13: #1 total tags in treatment: 22282687 INFO @ Thu, 09 Dec 2021 00:40:13: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:40:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:40:13: #1 tags after filtering in treatment: 22282687 INFO @ Thu, 09 Dec 2021 00:40:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:40:13: #1 finished! INFO @ Thu, 09 Dec 2021 00:40:13: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:40:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:40:15: #2 number of paired peaks: 118 WARNING @ Thu, 09 Dec 2021 00:40:15: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Thu, 09 Dec 2021 00:40:15: start model_add_line... INFO @ Thu, 09 Dec 2021 00:40:15: start X-correlation... INFO @ Thu, 09 Dec 2021 00:40:15: end of X-cor INFO @ Thu, 09 Dec 2021 00:40:15: #2 finished! INFO @ Thu, 09 Dec 2021 00:40:15: #2 predicted fragment length is 47 bps INFO @ Thu, 09 Dec 2021 00:40:15: #2 alternative fragment length(s) may be 2,47,598 bps INFO @ Thu, 09 Dec 2021 00:40:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.10_model.r WARNING @ Thu, 09 Dec 2021 00:40:15: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:40:15: #2 You may need to consider one of the other alternative d(s): 2,47,598 WARNING @ Thu, 09 Dec 2021 00:40:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 00:40:15: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:40:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:40:17: 17000000 INFO @ Thu, 09 Dec 2021 00:40:19: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:40:22: 18000000 INFO @ Thu, 09 Dec 2021 00:40:27: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:40:31: 20000000 INFO @ Thu, 09 Dec 2021 00:40:36: 21000000 INFO @ Thu, 09 Dec 2021 00:40:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:40:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:40:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.05_summits.bed INFO @ Thu, 09 Dec 2021 00:40:36: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4954 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:40:40: 22000000 INFO @ Thu, 09 Dec 2021 00:40:42: #1 tag size is determined as 49 bps INFO @ Thu, 09 Dec 2021 00:40:42: #1 tag size = 49 INFO @ Thu, 09 Dec 2021 00:40:42: #1 total tags in treatment: 22282687 INFO @ Thu, 09 Dec 2021 00:40:42: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:40:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:40:42: #1 tags after filtering in treatment: 22282687 INFO @ Thu, 09 Dec 2021 00:40:42: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 00:40:42: #1 finished! INFO @ Thu, 09 Dec 2021 00:40:42: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:40:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:40:43: #2 number of paired peaks: 118 WARNING @ Thu, 09 Dec 2021 00:40:43: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Thu, 09 Dec 2021 00:40:43: start model_add_line... INFO @ Thu, 09 Dec 2021 00:40:43: start X-correlation... INFO @ Thu, 09 Dec 2021 00:40:44: end of X-cor INFO @ Thu, 09 Dec 2021 00:40:44: #2 finished! INFO @ Thu, 09 Dec 2021 00:40:44: #2 predicted fragment length is 47 bps INFO @ Thu, 09 Dec 2021 00:40:44: #2 alternative fragment length(s) may be 2,47,598 bps INFO @ Thu, 09 Dec 2021 00:40:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.20_model.r WARNING @ Thu, 09 Dec 2021 00:40:44: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:40:44: #2 You may need to consider one of the other alternative d(s): 2,47,598 WARNING @ Thu, 09 Dec 2021 00:40:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 00:40:44: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:40:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:40:49: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:41:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:41:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:41:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.10_summits.bed INFO @ Thu, 09 Dec 2021 00:41:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1433 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:41:18: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:41:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:41:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:41:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8832063/SRX8832063.20_summits.bed INFO @ Thu, 09 Dec 2021 00:41:36: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (177 records, 4 fields): 2 millis CompletedMACS2peakCalling