Job ID = 10165631 SRX = SRX6799188 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 36477308 spots for SRR10065395/SRR10065395.sra Written 36477308 spots for SRR10065395/SRR10065395.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165900 ("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: 00:08:22 36477308 reads; of these: 36477308 (100.00%) were unpaired; of these: 565013 (1.55%) aligned 0 times 25323624 (69.42%) aligned exactly 1 time 10588671 (29.03%) aligned >1 times 98.45% overall alignment rate Time searching: 00:08:22 Overall time: 00:08:22 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] 11965674 / 35912295 = 0.3332 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 19:47:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.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, 08 Oct 2020 19:47:45: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:47:45: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:47:51: 1000000 INFO @ Thu, 08 Oct 2020 19:47:58: 2000000 INFO @ Thu, 08 Oct 2020 19:48:04: 3000000 INFO @ Thu, 08 Oct 2020 19:48:10: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 19:48:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.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, 08 Oct 2020 19:48:15: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:48:15: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:48:17: 5000000 INFO @ Thu, 08 Oct 2020 19:48:22: 1000000 INFO @ Thu, 08 Oct 2020 19:48:24: 6000000 INFO @ Thu, 08 Oct 2020 19:48:29: 2000000 INFO @ Thu, 08 Oct 2020 19:48:31: 7000000 INFO @ Thu, 08 Oct 2020 19:48:36: 3000000 INFO @ Thu, 08 Oct 2020 19:48:38: 8000000 INFO @ Thu, 08 Oct 2020 19:48:42: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 08 Oct 2020 19:48:45: 9000000 INFO @ Thu, 08 Oct 2020 19:48:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.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, 08 Oct 2020 19:48:45: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:48:45: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:48:49: 5000000 INFO @ Thu, 08 Oct 2020 19:48:51: 1000000 INFO @ Thu, 08 Oct 2020 19:48:52: 10000000 INFO @ Thu, 08 Oct 2020 19:48:56: 6000000 INFO @ Thu, 08 Oct 2020 19:48:58: 2000000 INFO @ Thu, 08 Oct 2020 19:48:59: 11000000 INFO @ Thu, 08 Oct 2020 19:49:03: 7000000 INFO @ Thu, 08 Oct 2020 19:49:04: 3000000 INFO @ Thu, 08 Oct 2020 19:49:06: 12000000 INFO @ Thu, 08 Oct 2020 19:49:10: 8000000 INFO @ Thu, 08 Oct 2020 19:49:10: 4000000 INFO @ Thu, 08 Oct 2020 19:49:13: 13000000 INFO @ Thu, 08 Oct 2020 19:49:16: 5000000 INFO @ Thu, 08 Oct 2020 19:49:17: 9000000 INFO @ Thu, 08 Oct 2020 19:49:21: 14000000 INFO @ Thu, 08 Oct 2020 19:49:23: 6000000 INFO @ Thu, 08 Oct 2020 19:49:24: 10000000 INFO @ Thu, 08 Oct 2020 19:49:28: 15000000 INFO @ Thu, 08 Oct 2020 19:49:29: 7000000 INFO @ Thu, 08 Oct 2020 19:49:31: 11000000 INFO @ Thu, 08 Oct 2020 19:49:35: 16000000 INFO @ Thu, 08 Oct 2020 19:49:35: 8000000 INFO @ Thu, 08 Oct 2020 19:49:38: 12000000 INFO @ Thu, 08 Oct 2020 19:49:42: 9000000 INFO @ Thu, 08 Oct 2020 19:49:42: 17000000 INFO @ Thu, 08 Oct 2020 19:49:45: 13000000 INFO @ Thu, 08 Oct 2020 19:49:48: 10000000 INFO @ Thu, 08 Oct 2020 19:49:49: 18000000 INFO @ Thu, 08 Oct 2020 19:49:52: 14000000 INFO @ Thu, 08 Oct 2020 19:49:54: 11000000 INFO @ Thu, 08 Oct 2020 19:49:56: 19000000 INFO @ Thu, 08 Oct 2020 19:49:58: 15000000 INFO @ Thu, 08 Oct 2020 19:50:00: 12000000 INFO @ Thu, 08 Oct 2020 19:50:03: 20000000 INFO @ Thu, 08 Oct 2020 19:50:05: 16000000 INFO @ Thu, 08 Oct 2020 19:50:07: 13000000 INFO @ Thu, 08 Oct 2020 19:50:11: 21000000 INFO @ Thu, 08 Oct 2020 19:50:12: 17000000 INFO @ Thu, 08 Oct 2020 19:50:13: 14000000 INFO @ Thu, 08 Oct 2020 19:50:18: 22000000 INFO @ Thu, 08 Oct 2020 19:50:19: 15000000 INFO @ Thu, 08 Oct 2020 19:50:19: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:50:25: 16000000 INFO @ Thu, 08 Oct 2020 19:50:26: 23000000 INFO @ Thu, 08 Oct 2020 19:50:26: 19000000 INFO @ Thu, 08 Oct 2020 19:50:32: 17000000 INFO @ Thu, 08 Oct 2020 19:50:33: 20000000 INFO @ Thu, 08 Oct 2020 19:50:33: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:50:33: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:50:33: #1 total tags in treatment: 23946621 INFO @ Thu, 08 Oct 2020 19:50:33: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:50:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:50:33: #1 tags after filtering in treatment: 23946621 INFO @ Thu, 08 Oct 2020 19:50:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:50:33: #1 finished! INFO @ Thu, 08 Oct 2020 19:50:33: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:50:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:50:34: #2 number of paired peaks: 385 WARNING @ Thu, 08 Oct 2020 19:50:34: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Thu, 08 Oct 2020 19:50:34: start model_add_line... INFO @ Thu, 08 Oct 2020 19:50:35: start X-correlation... INFO @ Thu, 08 Oct 2020 19:50:35: end of X-cor INFO @ Thu, 08 Oct 2020 19:50:35: #2 finished! INFO @ Thu, 08 Oct 2020 19:50:35: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 19:50:35: #2 alternative fragment length(s) may be 1 bps INFO @ Thu, 08 Oct 2020 19:50:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.05_model.r WARNING @ Thu, 08 Oct 2020 19:50:35: #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, 08 Oct 2020 19:50:35: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Thu, 08 Oct 2020 19:50:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:50:35: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:50:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:50:38: 18000000 INFO @ Thu, 08 Oct 2020 19:50:39: 21000000 INFO @ Thu, 08 Oct 2020 19:50:44: 19000000 INFO @ Thu, 08 Oct 2020 19:50:46: 22000000 INFO @ Thu, 08 Oct 2020 19:50:50: 20000000 INFO @ Thu, 08 Oct 2020 19:50:53: 23000000 INFO @ Thu, 08 Oct 2020 19:50:56: 21000000 INFO @ Thu, 08 Oct 2020 19:50:59: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:50:59: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:50:59: #1 total tags in treatment: 23946621 INFO @ Thu, 08 Oct 2020 19:50:59: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:50:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:50:59: #1 tags after filtering in treatment: 23946621 INFO @ Thu, 08 Oct 2020 19:50:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:50:59: #1 finished! INFO @ Thu, 08 Oct 2020 19:50:59: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:50:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:51:01: #2 number of paired peaks: 385 WARNING @ Thu, 08 Oct 2020 19:51:01: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Thu, 08 Oct 2020 19:51:01: start model_add_line... INFO @ Thu, 08 Oct 2020 19:51:01: start X-correlation... INFO @ Thu, 08 Oct 2020 19:51:01: end of X-cor INFO @ Thu, 08 Oct 2020 19:51:01: #2 finished! INFO @ Thu, 08 Oct 2020 19:51:01: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 19:51:01: #2 alternative fragment length(s) may be 1 bps INFO @ Thu, 08 Oct 2020 19:51:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.10_model.r WARNING @ Thu, 08 Oct 2020 19:51:01: #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, 08 Oct 2020 19:51:01: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Thu, 08 Oct 2020 19:51:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:51:01: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:51:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:51:02: 22000000 INFO @ Thu, 08 Oct 2020 19:51:07: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:51:07: 23000000 INFO @ Thu, 08 Oct 2020 19:51:13: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:51:13: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:51:13: #1 total tags in treatment: 23946621 INFO @ Thu, 08 Oct 2020 19:51:13: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:51:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:51:13: #1 tags after filtering in treatment: 23946621 INFO @ Thu, 08 Oct 2020 19:51:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:51:13: #1 finished! INFO @ Thu, 08 Oct 2020 19:51:13: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:51:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:51:15: #2 number of paired peaks: 385 WARNING @ Thu, 08 Oct 2020 19:51:15: Fewer paired peaks (385) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 385 pairs to build model! INFO @ Thu, 08 Oct 2020 19:51:15: start model_add_line... INFO @ Thu, 08 Oct 2020 19:51:15: start X-correlation... INFO @ Thu, 08 Oct 2020 19:51:15: end of X-cor INFO @ Thu, 08 Oct 2020 19:51:15: #2 finished! INFO @ Thu, 08 Oct 2020 19:51:15: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 19:51:15: #2 alternative fragment length(s) may be 1 bps INFO @ Thu, 08 Oct 2020 19:51:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.20_model.r WARNING @ Thu, 08 Oct 2020 19:51:15: #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, 08 Oct 2020 19:51:15: #2 You may need to consider one of the other alternative d(s): 1 WARNING @ Thu, 08 Oct 2020 19:51:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:51:15: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:51:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:51:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:51:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:51:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.05_summits.bed INFO @ Thu, 08 Oct 2020 19:51:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:51:34: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:51:48: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:51:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:51:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:51:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.10_summits.bed INFO @ Thu, 08 Oct 2020 19:51:49: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:52:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:52:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:52:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799188/SRX6799188.20_summits.bed INFO @ Thu, 08 Oct 2020 19:52:02: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling