Job ID = 14160500 SRX = SRX8331147 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 30081170 spots for SRR11778460/SRR11778460.sra Written 30081170 spots for SRR11778460/SRR11778460.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160659 ("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: 00:14:37 30081170 reads; of these: 30081170 (100.00%) were unpaired; of these: 684867 (2.28%) aligned 0 times 24947261 (82.93%) aligned exactly 1 time 4449042 (14.79%) aligned >1 times 97.72% overall alignment rate Time searching: 00:14:38 Overall time: 00:14:38 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] 7603447 / 29396303 = 0.2587 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 03:21:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.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 03:21:42: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:21:42: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:21:51: 1000000 INFO @ Thu, 09 Dec 2021 03:21:59: 2000000 INFO @ Thu, 09 Dec 2021 03:22:07: 3000000 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 03:22:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.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 03:22:12: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:22:12: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:22:15: 4000000 INFO @ Thu, 09 Dec 2021 03:22:21: 1000000 INFO @ Thu, 09 Dec 2021 03:22:23: 5000000 INFO @ Thu, 09 Dec 2021 03:22:29: 2000000 INFO @ Thu, 09 Dec 2021 03:22:32: 6000000 INFO @ Thu, 09 Dec 2021 03:22:38: 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 @ Thu, 09 Dec 2021 03:22:41: 7000000 INFO @ Thu, 09 Dec 2021 03:22:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.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 03:22:42: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:22:42: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:22:48: 4000000 INFO @ Thu, 09 Dec 2021 03:22:50: 8000000 INFO @ Thu, 09 Dec 2021 03:22:52: 1000000 INFO @ Thu, 09 Dec 2021 03:22:57: 5000000 INFO @ Thu, 09 Dec 2021 03:23:00: 9000000 INFO @ Thu, 09 Dec 2021 03:23:01: 2000000 INFO @ Thu, 09 Dec 2021 03:23:07: 6000000 INFO @ Thu, 09 Dec 2021 03:23:10: 10000000 INFO @ Thu, 09 Dec 2021 03:23:10: 3000000 INFO @ Thu, 09 Dec 2021 03:23:16: 7000000 INFO @ Thu, 09 Dec 2021 03:23:19: 11000000 INFO @ Thu, 09 Dec 2021 03:23:20: 4000000 INFO @ Thu, 09 Dec 2021 03:23:25: 8000000 INFO @ Thu, 09 Dec 2021 03:23:28: 12000000 INFO @ Thu, 09 Dec 2021 03:23:29: 5000000 INFO @ Thu, 09 Dec 2021 03:23:34: 9000000 INFO @ Thu, 09 Dec 2021 03:23:37: 13000000 INFO @ Thu, 09 Dec 2021 03:23:38: 6000000 INFO @ Thu, 09 Dec 2021 03:23:43: 10000000 INFO @ Thu, 09 Dec 2021 03:23:47: 14000000 INFO @ Thu, 09 Dec 2021 03:23:47: 7000000 INFO @ Thu, 09 Dec 2021 03:23:52: 11000000 INFO @ Thu, 09 Dec 2021 03:23:56: 15000000 INFO @ Thu, 09 Dec 2021 03:23:57: 8000000 INFO @ Thu, 09 Dec 2021 03:24:02: 12000000 INFO @ Thu, 09 Dec 2021 03:24:06: 16000000 INFO @ Thu, 09 Dec 2021 03:24:06: 9000000 INFO @ Thu, 09 Dec 2021 03:24:11: 13000000 INFO @ Thu, 09 Dec 2021 03:24:15: 17000000 INFO @ Thu, 09 Dec 2021 03:24:15: 10000000 INFO @ Thu, 09 Dec 2021 03:24:20: 14000000 INFO @ Thu, 09 Dec 2021 03:24:24: 18000000 INFO @ Thu, 09 Dec 2021 03:24:24: 11000000 INFO @ Thu, 09 Dec 2021 03:24:29: 15000000 INFO @ Thu, 09 Dec 2021 03:24:32: 19000000 INFO @ Thu, 09 Dec 2021 03:24:33: 12000000 INFO @ Thu, 09 Dec 2021 03:24:37: 16000000 INFO @ Thu, 09 Dec 2021 03:24:40: 20000000 INFO @ Thu, 09 Dec 2021 03:24:42: 13000000 INFO @ Thu, 09 Dec 2021 03:24:45: 17000000 INFO @ Thu, 09 Dec 2021 03:24:49: 21000000 INFO @ Thu, 09 Dec 2021 03:24:50: 14000000 INFO @ Thu, 09 Dec 2021 03:24:53: 18000000 INFO @ Thu, 09 Dec 2021 03:24:55: #1 tag size is determined as 68 bps INFO @ Thu, 09 Dec 2021 03:24:55: #1 tag size = 68 INFO @ Thu, 09 Dec 2021 03:24:55: #1 total tags in treatment: 21792856 INFO @ Thu, 09 Dec 2021 03:24:55: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:24:55: #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 03:24:56: #1 tags after filtering in treatment: 21792856 INFO @ Thu, 09 Dec 2021 03:24:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:24:56: #1 finished! INFO @ Thu, 09 Dec 2021 03:24:56: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:24:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:24:58: #2 number of paired peaks: 149 WARNING @ Thu, 09 Dec 2021 03:24:58: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Thu, 09 Dec 2021 03:24:58: start model_add_line... INFO @ Thu, 09 Dec 2021 03:24:58: start X-correlation... INFO @ Thu, 09 Dec 2021 03:24:58: end of X-cor INFO @ Thu, 09 Dec 2021 03:24:58: #2 finished! INFO @ Thu, 09 Dec 2021 03:24:58: #2 predicted fragment length is 1 bps INFO @ Thu, 09 Dec 2021 03:24:58: #2 alternative fragment length(s) may be 1,11,468,537 bps INFO @ Thu, 09 Dec 2021 03:24:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.05_model.r WARNING @ Thu, 09 Dec 2021 03:24:58: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:24:58: #2 You may need to consider one of the other alternative d(s): 1,11,468,537 WARNING @ Thu, 09 Dec 2021 03:24:58: #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 03:24:58: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:24:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:24:59: 15000000 INFO @ Thu, 09 Dec 2021 03:25:02: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:25:08: 16000000 INFO @ Thu, 09 Dec 2021 03:25:10: 20000000 INFO @ Thu, 09 Dec 2021 03:25:17: 17000000 INFO @ Thu, 09 Dec 2021 03:25:18: 21000000 INFO @ Thu, 09 Dec 2021 03:25:24: #1 tag size is determined as 68 bps INFO @ Thu, 09 Dec 2021 03:25:24: #1 tag size = 68 INFO @ Thu, 09 Dec 2021 03:25:24: #1 total tags in treatment: 21792856 INFO @ Thu, 09 Dec 2021 03:25:24: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:25:24: #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 03:25:25: #1 tags after filtering in treatment: 21792856 INFO @ Thu, 09 Dec 2021 03:25:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:25:25: #1 finished! INFO @ Thu, 09 Dec 2021 03:25:25: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:25:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:25:26: 18000000 INFO @ Thu, 09 Dec 2021 03:25:26: #2 number of paired peaks: 149 WARNING @ Thu, 09 Dec 2021 03:25:26: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Thu, 09 Dec 2021 03:25:26: start model_add_line... INFO @ Thu, 09 Dec 2021 03:25:27: start X-correlation... INFO @ Thu, 09 Dec 2021 03:25:27: end of X-cor INFO @ Thu, 09 Dec 2021 03:25:27: #2 finished! INFO @ Thu, 09 Dec 2021 03:25:27: #2 predicted fragment length is 1 bps INFO @ Thu, 09 Dec 2021 03:25:27: #2 alternative fragment length(s) may be 1,11,468,537 bps INFO @ Thu, 09 Dec 2021 03:25:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.10_model.r WARNING @ Thu, 09 Dec 2021 03:25:27: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:25:27: #2 You may need to consider one of the other alternative d(s): 1,11,468,537 WARNING @ Thu, 09 Dec 2021 03:25:27: #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 03:25:27: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:25:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:25:35: 19000000 INFO @ Thu, 09 Dec 2021 03:25:43: 20000000 INFO @ Thu, 09 Dec 2021 03:25:44: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:25:52: 21000000 INFO @ Thu, 09 Dec 2021 03:25:59: #1 tag size is determined as 68 bps INFO @ Thu, 09 Dec 2021 03:25:59: #1 tag size = 68 INFO @ Thu, 09 Dec 2021 03:25:59: #1 total tags in treatment: 21792856 INFO @ Thu, 09 Dec 2021 03:25:59: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:25:59: #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 03:26:00: #1 tags after filtering in treatment: 21792856 INFO @ Thu, 09 Dec 2021 03:26:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 09 Dec 2021 03:26:00: #1 finished! INFO @ Thu, 09 Dec 2021 03:26:00: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:26:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:26:01: #2 number of paired peaks: 149 WARNING @ Thu, 09 Dec 2021 03:26:01: Fewer paired peaks (149) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 149 pairs to build model! INFO @ Thu, 09 Dec 2021 03:26:01: start model_add_line... INFO @ Thu, 09 Dec 2021 03:26:02: start X-correlation... INFO @ Thu, 09 Dec 2021 03:26:02: end of X-cor INFO @ Thu, 09 Dec 2021 03:26:02: #2 finished! INFO @ Thu, 09 Dec 2021 03:26:02: #2 predicted fragment length is 1 bps INFO @ Thu, 09 Dec 2021 03:26:02: #2 alternative fragment length(s) may be 1,11,468,537 bps INFO @ Thu, 09 Dec 2021 03:26:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.20_model.r WARNING @ Thu, 09 Dec 2021 03:26:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:26:02: #2 You may need to consider one of the other alternative d(s): 1,11,468,537 WARNING @ Thu, 09 Dec 2021 03:26:02: #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 03:26:02: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:26:02: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:26:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:26:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:26:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.05_summits.bed INFO @ Thu, 09 Dec 2021 03:26:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:26:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:26:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:26:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:26:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.10_summits.bed INFO @ Thu, 09 Dec 2021 03:26:35: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:26:47: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:27:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:27:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:27:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8331147/SRX8331147.20_summits.bed INFO @ Thu, 09 Dec 2021 03:27:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling