Job ID = 14159518 SRX = SRX8845631 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 49002203 spots for SRR12345938/SRR12345938.sra Written 49002203 spots for SRR12345938/SRR12345938.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159696 ("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: 00:07:23 49002203 reads; of these: 49002203 (100.00%) were unpaired; of these: 24832552 (50.68%) aligned 0 times 19874820 (40.56%) aligned exactly 1 time 4294831 (8.76%) aligned >1 times 49.32% overall alignment rate Time searching: 00:07:23 Overall time: 00:07:23 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] 3098850 / 24169651 = 0.1282 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 22:32:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.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 22:32:02: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:32:02: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:32:08: 1000000 INFO @ Wed, 08 Dec 2021 22:32:15: 2000000 INFO @ Wed, 08 Dec 2021 22:32:21: 3000000 INFO @ Wed, 08 Dec 2021 22:32:27: 4000000 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 22:32:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.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 22:32:32: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:32:32: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:32:33: 5000000 INFO @ Wed, 08 Dec 2021 22:32:38: 1000000 INFO @ Wed, 08 Dec 2021 22:32:40: 6000000 INFO @ Wed, 08 Dec 2021 22:32:45: 2000000 INFO @ Wed, 08 Dec 2021 22:32:47: 7000000 INFO @ Wed, 08 Dec 2021 22:32:51: 3000000 INFO @ Wed, 08 Dec 2021 22:32:53: 8000000 INFO @ Wed, 08 Dec 2021 22:32:57: 4000000 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 22:33:00: 9000000 INFO @ Wed, 08 Dec 2021 22:33:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.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 22:33:02: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:33:02: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:33:04: 5000000 INFO @ Wed, 08 Dec 2021 22:33:07: 10000000 INFO @ Wed, 08 Dec 2021 22:33:08: 1000000 INFO @ Wed, 08 Dec 2021 22:33:10: 6000000 INFO @ Wed, 08 Dec 2021 22:33:14: 11000000 INFO @ Wed, 08 Dec 2021 22:33:15: 2000000 INFO @ Wed, 08 Dec 2021 22:33:17: 7000000 INFO @ Wed, 08 Dec 2021 22:33:21: 12000000 INFO @ Wed, 08 Dec 2021 22:33:21: 3000000 INFO @ Wed, 08 Dec 2021 22:33:23: 8000000 INFO @ Wed, 08 Dec 2021 22:33:28: 4000000 INFO @ Wed, 08 Dec 2021 22:33:28: 13000000 INFO @ Wed, 08 Dec 2021 22:33:30: 9000000 INFO @ Wed, 08 Dec 2021 22:33:34: 5000000 INFO @ Wed, 08 Dec 2021 22:33:35: 14000000 INFO @ Wed, 08 Dec 2021 22:33:36: 10000000 INFO @ Wed, 08 Dec 2021 22:33:41: 6000000 INFO @ Wed, 08 Dec 2021 22:33:42: 15000000 INFO @ Wed, 08 Dec 2021 22:33:42: 11000000 INFO @ Wed, 08 Dec 2021 22:33:47: 7000000 INFO @ Wed, 08 Dec 2021 22:33:49: 12000000 INFO @ Wed, 08 Dec 2021 22:33:49: 16000000 INFO @ Wed, 08 Dec 2021 22:33:53: 8000000 INFO @ Wed, 08 Dec 2021 22:33:55: 13000000 INFO @ Wed, 08 Dec 2021 22:33:56: 17000000 INFO @ Wed, 08 Dec 2021 22:34:00: 9000000 INFO @ Wed, 08 Dec 2021 22:34:02: 14000000 INFO @ Wed, 08 Dec 2021 22:34:03: 18000000 INFO @ Wed, 08 Dec 2021 22:34:06: 10000000 INFO @ Wed, 08 Dec 2021 22:34:08: 15000000 INFO @ Wed, 08 Dec 2021 22:34:10: 19000000 INFO @ Wed, 08 Dec 2021 22:34:13: 11000000 INFO @ Wed, 08 Dec 2021 22:34:15: 16000000 INFO @ Wed, 08 Dec 2021 22:34:17: 20000000 INFO @ Wed, 08 Dec 2021 22:34:19: 12000000 INFO @ Wed, 08 Dec 2021 22:34:21: 17000000 INFO @ Wed, 08 Dec 2021 22:34:23: 21000000 INFO @ Wed, 08 Dec 2021 22:34:24: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 22:34:24: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 22:34:24: #1 total tags in treatment: 21070801 INFO @ Wed, 08 Dec 2021 22:34:24: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:34:24: #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 22:34:24: #1 tags after filtering in treatment: 21070801 INFO @ Wed, 08 Dec 2021 22:34:24: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:34:24: #1 finished! INFO @ Wed, 08 Dec 2021 22:34:24: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:34:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:34:25: 13000000 INFO @ Wed, 08 Dec 2021 22:34:26: #2 number of paired peaks: 174 WARNING @ Wed, 08 Dec 2021 22:34:26: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Wed, 08 Dec 2021 22:34:26: start model_add_line... INFO @ Wed, 08 Dec 2021 22:34:26: start X-correlation... INFO @ Wed, 08 Dec 2021 22:34:26: end of X-cor INFO @ Wed, 08 Dec 2021 22:34:26: #2 finished! INFO @ Wed, 08 Dec 2021 22:34:26: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 22:34:26: #2 alternative fragment length(s) may be 1,24,43 bps INFO @ Wed, 08 Dec 2021 22:34:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.05_model.r WARNING @ Wed, 08 Dec 2021 22:34:26: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:34:26: #2 You may need to consider one of the other alternative d(s): 1,24,43 WARNING @ Wed, 08 Dec 2021 22:34:26: #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 22:34:26: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:34:26: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:34:28: 18000000 INFO @ Wed, 08 Dec 2021 22:34:32: 14000000 INFO @ Wed, 08 Dec 2021 22:34:34: 19000000 INFO @ Wed, 08 Dec 2021 22:34:38: 15000000 INFO @ Wed, 08 Dec 2021 22:34:40: 20000000 INFO @ Wed, 08 Dec 2021 22:34:45: 16000000 INFO @ Wed, 08 Dec 2021 22:34:47: 21000000 INFO @ Wed, 08 Dec 2021 22:34:47: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 22:34:47: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 22:34:47: #1 total tags in treatment: 21070801 INFO @ Wed, 08 Dec 2021 22:34:47: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:34:47: #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 22:34:48: #1 tags after filtering in treatment: 21070801 INFO @ Wed, 08 Dec 2021 22:34:48: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:34:48: #1 finished! INFO @ Wed, 08 Dec 2021 22:34:48: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:34:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:34:49: #2 number of paired peaks: 174 WARNING @ Wed, 08 Dec 2021 22:34:49: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Wed, 08 Dec 2021 22:34:49: start model_add_line... INFO @ Wed, 08 Dec 2021 22:34:49: start X-correlation... INFO @ Wed, 08 Dec 2021 22:34:49: end of X-cor INFO @ Wed, 08 Dec 2021 22:34:49: #2 finished! INFO @ Wed, 08 Dec 2021 22:34:49: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 22:34:49: #2 alternative fragment length(s) may be 1,24,43 bps INFO @ Wed, 08 Dec 2021 22:34:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.10_model.r WARNING @ Wed, 08 Dec 2021 22:34:49: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:34:49: #2 You may need to consider one of the other alternative d(s): 1,24,43 WARNING @ Wed, 08 Dec 2021 22:34:49: #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 22:34:49: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:34:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:34:51: 17000000 INFO @ Wed, 08 Dec 2021 22:34:57: 18000000 INFO @ Wed, 08 Dec 2021 22:34:58: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:35:02: 19000000 INFO @ Wed, 08 Dec 2021 22:35:08: 20000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:35:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:35:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:35:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.05_summits.bed INFO @ Wed, 08 Dec 2021 22:35:13: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:35:14: 21000000 INFO @ Wed, 08 Dec 2021 22:35:14: #1 tag size is determined as 50 bps INFO @ Wed, 08 Dec 2021 22:35:14: #1 tag size = 50 INFO @ Wed, 08 Dec 2021 22:35:14: #1 total tags in treatment: 21070801 INFO @ Wed, 08 Dec 2021 22:35:14: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:35:14: #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 22:35:14: #1 tags after filtering in treatment: 21070801 INFO @ Wed, 08 Dec 2021 22:35:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 22:35:14: #1 finished! INFO @ Wed, 08 Dec 2021 22:35:14: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:35:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:35:16: #2 number of paired peaks: 174 WARNING @ Wed, 08 Dec 2021 22:35:16: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Wed, 08 Dec 2021 22:35:16: start model_add_line... INFO @ Wed, 08 Dec 2021 22:35:16: start X-correlation... INFO @ Wed, 08 Dec 2021 22:35:16: end of X-cor INFO @ Wed, 08 Dec 2021 22:35:16: #2 finished! INFO @ Wed, 08 Dec 2021 22:35:16: #2 predicted fragment length is 1 bps INFO @ Wed, 08 Dec 2021 22:35:16: #2 alternative fragment length(s) may be 1,24,43 bps INFO @ Wed, 08 Dec 2021 22:35:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.20_model.r WARNING @ Wed, 08 Dec 2021 22:35:16: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 22:35:16: #2 You may need to consider one of the other alternative d(s): 1,24,43 WARNING @ Wed, 08 Dec 2021 22:35:16: #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 22:35:16: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:35:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:35:21: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:35:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:35:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:35:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.10_summits.bed INFO @ Wed, 08 Dec 2021 22:35:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:35:47: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:36:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:36:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:36:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8845631/SRX8845631.20_summits.bed INFO @ Wed, 08 Dec 2021 22:36:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling