Job ID = 16434838 SRX = SRX10435512 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 32657675 spots for SRR14060944/SRR14060944.sra Written 32657675 spots for SRR14060944/SRR14060944.sra fastq に変換しました。 bowtie でマッピング中... Your job 16434916 ("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: 00:10:12 32657675 reads; of these: 32657675 (100.00%) were unpaired; of these: 923252 (2.83%) aligned 0 times 26668054 (81.66%) aligned exactly 1 time 5066369 (15.51%) aligned >1 times 97.17% overall alignment rate Time searching: 00:10:12 Overall time: 00:10:12 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] 5217273 / 31734423 = 0.1644 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 10:16:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.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 10:16:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:16:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:16:55: 1000000 INFO @ Tue, 02 Aug 2022 10:17:00: 2000000 INFO @ Tue, 02 Aug 2022 10:17:06: 3000000 INFO @ Tue, 02 Aug 2022 10:17:12: 4000000 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 10:17:18: 5000000 INFO @ Tue, 02 Aug 2022 10:17:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.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 10:17:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:17:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:17:24: 6000000 INFO @ Tue, 02 Aug 2022 10:17:25: 1000000 INFO @ Tue, 02 Aug 2022 10:17:30: 7000000 INFO @ Tue, 02 Aug 2022 10:17:31: 2000000 INFO @ Tue, 02 Aug 2022 10:17:36: 8000000 INFO @ Tue, 02 Aug 2022 10:17:37: 3000000 INFO @ Tue, 02 Aug 2022 10:17:42: 9000000 INFO @ Tue, 02 Aug 2022 10:17:43: 4000000 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 10:17:48: 10000000 INFO @ Tue, 02 Aug 2022 10:17:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.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 10:17:49: #1 read tag files... INFO @ Tue, 02 Aug 2022 10:17:49: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 10:17:49: 5000000 INFO @ Tue, 02 Aug 2022 10:17:54: 11000000 INFO @ Tue, 02 Aug 2022 10:17:55: 1000000 INFO @ Tue, 02 Aug 2022 10:17:55: 6000000 INFO @ Tue, 02 Aug 2022 10:18:00: 12000000 INFO @ Tue, 02 Aug 2022 10:18:01: 2000000 INFO @ Tue, 02 Aug 2022 10:18:01: 7000000 INFO @ Tue, 02 Aug 2022 10:18:06: 13000000 INFO @ Tue, 02 Aug 2022 10:18:07: 3000000 INFO @ Tue, 02 Aug 2022 10:18:07: 8000000 INFO @ Tue, 02 Aug 2022 10:18:12: 14000000 INFO @ Tue, 02 Aug 2022 10:18:13: 4000000 INFO @ Tue, 02 Aug 2022 10:18:13: 9000000 INFO @ Tue, 02 Aug 2022 10:18:18: 15000000 INFO @ Tue, 02 Aug 2022 10:18:19: 5000000 INFO @ Tue, 02 Aug 2022 10:18:19: 10000000 INFO @ Tue, 02 Aug 2022 10:18:24: 16000000 INFO @ Tue, 02 Aug 2022 10:18:25: 6000000 INFO @ Tue, 02 Aug 2022 10:18:25: 11000000 INFO @ Tue, 02 Aug 2022 10:18:30: 17000000 INFO @ Tue, 02 Aug 2022 10:18:31: 12000000 INFO @ Tue, 02 Aug 2022 10:18:31: 7000000 INFO @ Tue, 02 Aug 2022 10:18:36: 18000000 INFO @ Tue, 02 Aug 2022 10:18:37: 13000000 INFO @ Tue, 02 Aug 2022 10:18:37: 8000000 INFO @ Tue, 02 Aug 2022 10:18:41: 19000000 INFO @ Tue, 02 Aug 2022 10:18:42: 14000000 INFO @ Tue, 02 Aug 2022 10:18:43: 9000000 INFO @ Tue, 02 Aug 2022 10:18:47: 20000000 INFO @ Tue, 02 Aug 2022 10:18:48: 15000000 INFO @ Tue, 02 Aug 2022 10:18:49: 10000000 INFO @ Tue, 02 Aug 2022 10:18:54: 21000000 INFO @ Tue, 02 Aug 2022 10:18:54: 16000000 INFO @ Tue, 02 Aug 2022 10:18:55: 11000000 INFO @ Tue, 02 Aug 2022 10:19:00: 17000000 INFO @ Tue, 02 Aug 2022 10:19:00: 22000000 INFO @ Tue, 02 Aug 2022 10:19:01: 12000000 INFO @ Tue, 02 Aug 2022 10:19:05: 18000000 INFO @ Tue, 02 Aug 2022 10:19:06: 23000000 INFO @ Tue, 02 Aug 2022 10:19:07: 13000000 INFO @ Tue, 02 Aug 2022 10:19:11: 19000000 INFO @ Tue, 02 Aug 2022 10:19:12: 24000000 INFO @ Tue, 02 Aug 2022 10:19:12: 14000000 INFO @ Tue, 02 Aug 2022 10:19:17: 20000000 INFO @ Tue, 02 Aug 2022 10:19:18: 25000000 INFO @ Tue, 02 Aug 2022 10:19:18: 15000000 INFO @ Tue, 02 Aug 2022 10:19:23: 21000000 INFO @ Tue, 02 Aug 2022 10:19:24: 16000000 INFO @ Tue, 02 Aug 2022 10:19:24: 26000000 INFO @ Tue, 02 Aug 2022 10:19:27: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:19:27: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:19:27: #1 total tags in treatment: 26517150 INFO @ Tue, 02 Aug 2022 10:19:27: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:19:27: #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 10:19:27: #1 tags after filtering in treatment: 26517150 INFO @ Tue, 02 Aug 2022 10:19:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:19:27: #1 finished! INFO @ Tue, 02 Aug 2022 10:19:27: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:19:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:19:29: 22000000 INFO @ Tue, 02 Aug 2022 10:19:29: #2 number of paired peaks: 101 WARNING @ Tue, 02 Aug 2022 10:19:29: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Tue, 02 Aug 2022 10:19:29: start model_add_line... INFO @ Tue, 02 Aug 2022 10:19:29: start X-correlation... INFO @ Tue, 02 Aug 2022 10:19:29: end of X-cor INFO @ Tue, 02 Aug 2022 10:19:29: #2 finished! INFO @ Tue, 02 Aug 2022 10:19:29: #2 predicted fragment length is 1 bps INFO @ Tue, 02 Aug 2022 10:19:29: #2 alternative fragment length(s) may be 1,26,34,73,565,587 bps INFO @ Tue, 02 Aug 2022 10:19:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.05_model.r WARNING @ Tue, 02 Aug 2022 10:19:29: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:19:29: #2 You may need to consider one of the other alternative d(s): 1,26,34,73,565,587 WARNING @ Tue, 02 Aug 2022 10:19:29: #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 10:19:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:19:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:19:30: 17000000 INFO @ Tue, 02 Aug 2022 10:19:34: 23000000 INFO @ Tue, 02 Aug 2022 10:19:35: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 10:19:40: 24000000 INFO @ Tue, 02 Aug 2022 10:19:41: 19000000 INFO @ Tue, 02 Aug 2022 10:19:46: 25000000 INFO @ Tue, 02 Aug 2022 10:19:47: 20000000 INFO @ Tue, 02 Aug 2022 10:19:52: 26000000 INFO @ Tue, 02 Aug 2022 10:19:53: 21000000 INFO @ Tue, 02 Aug 2022 10:19:55: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:19:55: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:19:55: #1 total tags in treatment: 26517150 INFO @ Tue, 02 Aug 2022 10:19:55: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:19:55: #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 10:19:55: #1 tags after filtering in treatment: 26517150 INFO @ Tue, 02 Aug 2022 10:19:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:19:55: #1 finished! INFO @ Tue, 02 Aug 2022 10:19:55: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:19:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:19:57: #2 number of paired peaks: 101 WARNING @ Tue, 02 Aug 2022 10:19:57: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Tue, 02 Aug 2022 10:19:57: start model_add_line... INFO @ Tue, 02 Aug 2022 10:19:57: start X-correlation... INFO @ Tue, 02 Aug 2022 10:19:57: end of X-cor INFO @ Tue, 02 Aug 2022 10:19:57: #2 finished! INFO @ Tue, 02 Aug 2022 10:19:57: #2 predicted fragment length is 1 bps INFO @ Tue, 02 Aug 2022 10:19:57: #2 alternative fragment length(s) may be 1,26,34,73,565,587 bps INFO @ Tue, 02 Aug 2022 10:19:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.10_model.r WARNING @ Tue, 02 Aug 2022 10:19:57: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:19:57: #2 You may need to consider one of the other alternative d(s): 1,26,34,73,565,587 WARNING @ Tue, 02 Aug 2022 10:19:57: #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 10:19:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:19:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 10:19:58: 22000000 INFO @ Tue, 02 Aug 2022 10:20:04: 23000000 INFO @ Tue, 02 Aug 2022 10:20:07: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:20:09: 24000000 INFO @ Tue, 02 Aug 2022 10:20:14: 25000000 INFO @ Tue, 02 Aug 2022 10:20:20: 26000000 INFO @ Tue, 02 Aug 2022 10:20:23: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 10:20:23: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 10:20:23: #1 total tags in treatment: 26517150 INFO @ Tue, 02 Aug 2022 10:20:23: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 10:20:23: #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 10:20:23: #1 tags after filtering in treatment: 26517150 INFO @ Tue, 02 Aug 2022 10:20:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 10:20:23: #1 finished! INFO @ Tue, 02 Aug 2022 10:20:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 10:20:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 10:20:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.05_peaks.xls INFO @ Tue, 02 Aug 2022 10:20:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:20:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.05_summits.bed INFO @ Tue, 02 Aug 2022 10:20:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:20:25: #2 number of paired peaks: 101 WARNING @ Tue, 02 Aug 2022 10:20:25: Fewer paired peaks (101) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 101 pairs to build model! INFO @ Tue, 02 Aug 2022 10:20:25: start model_add_line... INFO @ Tue, 02 Aug 2022 10:20:25: start X-correlation... INFO @ Tue, 02 Aug 2022 10:20:25: end of X-cor INFO @ Tue, 02 Aug 2022 10:20:25: #2 finished! INFO @ Tue, 02 Aug 2022 10:20:25: #2 predicted fragment length is 1 bps INFO @ Tue, 02 Aug 2022 10:20:25: #2 alternative fragment length(s) may be 1,26,34,73,565,587 bps INFO @ Tue, 02 Aug 2022 10:20:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.20_model.r WARNING @ Tue, 02 Aug 2022 10:20:25: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 10:20:25: #2 You may need to consider one of the other alternative d(s): 1,26,34,73,565,587 WARNING @ Tue, 02 Aug 2022 10:20:25: #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 10:20:25: #3 Call peaks... INFO @ Tue, 02 Aug 2022 10:20:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 10:20:35: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:20:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.10_peaks.xls INFO @ Tue, 02 Aug 2022 10:20:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:20:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.10_summits.bed INFO @ Tue, 02 Aug 2022 10:20:52: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 10:21:03: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 10:21:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.20_peaks.xls INFO @ Tue, 02 Aug 2022 10:21:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 10:21:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10435512/SRX10435512.20_summits.bed INFO @ Tue, 02 Aug 2022 10:21:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling