Job ID = 10165633 SRX = SRX6799190 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 34174635 spots for SRR10065397/SRR10065397.sra Written 34174635 spots for SRR10065397/SRR10065397.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165904 ("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: 00:08:23 34174635 reads; of these: 34174635 (100.00%) were unpaired; of these: 1373911 (4.02%) aligned 0 times 22951237 (67.16%) aligned exactly 1 time 9849487 (28.82%) aligned >1 times 95.98% overall alignment rate Time searching: 00:08:23 Overall time: 00:08:23 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 16 files... [bam_rmdupse_core] 10050366 / 32800724 = 0.3064 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 19:47:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.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 19:47:35: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:47:35: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:47:39: 1000000 INFO @ Thu, 08 Oct 2020 19:47:44: 2000000 INFO @ Thu, 08 Oct 2020 19:47:48: 3000000 INFO @ Thu, 08 Oct 2020 19:47:53: 4000000 INFO @ Thu, 08 Oct 2020 19:47:58: 5000000 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 19:48:02: 6000000 INFO @ Thu, 08 Oct 2020 19:48:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.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 19:48:04: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:48:04: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:48:07: 7000000 INFO @ Thu, 08 Oct 2020 19:48:09: 1000000 INFO @ Thu, 08 Oct 2020 19:48:11: 8000000 INFO @ Thu, 08 Oct 2020 19:48:13: 2000000 INFO @ Thu, 08 Oct 2020 19:48:16: 9000000 INFO @ Thu, 08 Oct 2020 19:48:18: 3000000 INFO @ Thu, 08 Oct 2020 19:48:20: 10000000 INFO @ Thu, 08 Oct 2020 19:48:22: 4000000 INFO @ Thu, 08 Oct 2020 19:48:25: 11000000 INFO @ Thu, 08 Oct 2020 19:48:27: 5000000 INFO @ Thu, 08 Oct 2020 19:48:30: 12000000 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 19:48:32: 6000000 INFO @ Thu, 08 Oct 2020 19:48:34: 13000000 INFO @ Thu, 08 Oct 2020 19:48:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.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 19:48:35: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:48:35: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:48:36: 7000000 INFO @ Thu, 08 Oct 2020 19:48:39: 14000000 INFO @ Thu, 08 Oct 2020 19:48:39: 1000000 INFO @ Thu, 08 Oct 2020 19:48:41: 8000000 INFO @ Thu, 08 Oct 2020 19:48:44: 15000000 INFO @ Thu, 08 Oct 2020 19:48:44: 2000000 INFO @ Thu, 08 Oct 2020 19:48:46: 9000000 INFO @ Thu, 08 Oct 2020 19:48:49: 16000000 INFO @ Thu, 08 Oct 2020 19:48:49: 3000000 INFO @ Thu, 08 Oct 2020 19:48:50: 10000000 INFO @ Thu, 08 Oct 2020 19:48:53: 17000000 INFO @ Thu, 08 Oct 2020 19:48:53: 4000000 INFO @ Thu, 08 Oct 2020 19:48:55: 11000000 INFO @ Thu, 08 Oct 2020 19:48:58: 18000000 INFO @ Thu, 08 Oct 2020 19:48:58: 5000000 INFO @ Thu, 08 Oct 2020 19:49:00: 12000000 INFO @ Thu, 08 Oct 2020 19:49:03: 19000000 INFO @ Thu, 08 Oct 2020 19:49:03: 6000000 INFO @ Thu, 08 Oct 2020 19:49:04: 13000000 INFO @ Thu, 08 Oct 2020 19:49:07: 20000000 INFO @ Thu, 08 Oct 2020 19:49:08: 7000000 INFO @ Thu, 08 Oct 2020 19:49:09: 14000000 INFO @ Thu, 08 Oct 2020 19:49:12: 21000000 INFO @ Thu, 08 Oct 2020 19:49:12: 8000000 INFO @ Thu, 08 Oct 2020 19:49:14: 15000000 INFO @ Thu, 08 Oct 2020 19:49:17: 22000000 INFO @ Thu, 08 Oct 2020 19:49:17: 9000000 INFO @ Thu, 08 Oct 2020 19:49:19: 16000000 INFO @ Thu, 08 Oct 2020 19:49:20: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 19:49:20: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 19:49:20: #1 total tags in treatment: 22750358 INFO @ Thu, 08 Oct 2020 19:49:20: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:49:20: #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 19:49:21: #1 tags after filtering in treatment: 22750358 INFO @ Thu, 08 Oct 2020 19:49:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:49:21: #1 finished! INFO @ Thu, 08 Oct 2020 19:49:21: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:49:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:49:22: 10000000 INFO @ Thu, 08 Oct 2020 19:49:22: #2 number of paired peaks: 405 WARNING @ Thu, 08 Oct 2020 19:49:22: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Thu, 08 Oct 2020 19:49:22: start model_add_line... INFO @ Thu, 08 Oct 2020 19:49:22: start X-correlation... INFO @ Thu, 08 Oct 2020 19:49:22: end of X-cor INFO @ Thu, 08 Oct 2020 19:49:22: #2 finished! INFO @ Thu, 08 Oct 2020 19:49:22: #2 predicted fragment length is 2 bps INFO @ Thu, 08 Oct 2020 19:49:22: #2 alternative fragment length(s) may be 2,19,37 bps INFO @ Thu, 08 Oct 2020 19:49:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.05_model.r WARNING @ Thu, 08 Oct 2020 19:49:22: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:49:22: #2 You may need to consider one of the other alternative d(s): 2,19,37 WARNING @ Thu, 08 Oct 2020 19:49:22: #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 19:49:22: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:49:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:49:23: 17000000 INFO @ Thu, 08 Oct 2020 19:49:27: 11000000 INFO @ Thu, 08 Oct 2020 19:49:28: 18000000 INFO @ Thu, 08 Oct 2020 19:49:32: 12000000 INFO @ Thu, 08 Oct 2020 19:49:33: 19000000 INFO @ Thu, 08 Oct 2020 19:49:36: 13000000 INFO @ Thu, 08 Oct 2020 19:49:38: 20000000 INFO @ Thu, 08 Oct 2020 19:49:41: 14000000 INFO @ Thu, 08 Oct 2020 19:49:42: 21000000 INFO @ Thu, 08 Oct 2020 19:49:46: 15000000 INFO @ Thu, 08 Oct 2020 19:49:47: 22000000 INFO @ Thu, 08 Oct 2020 19:49:51: 16000000 INFO @ Thu, 08 Oct 2020 19:49:51: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 19:49:51: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 19:49:51: #1 total tags in treatment: 22750358 INFO @ Thu, 08 Oct 2020 19:49:51: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:49:51: #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 19:49:51: #1 tags after filtering in treatment: 22750358 INFO @ Thu, 08 Oct 2020 19:49:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:49:51: #1 finished! INFO @ Thu, 08 Oct 2020 19:49:51: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:49:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:49:53: #2 number of paired peaks: 405 WARNING @ Thu, 08 Oct 2020 19:49:53: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Thu, 08 Oct 2020 19:49:53: start model_add_line... INFO @ Thu, 08 Oct 2020 19:49:53: start X-correlation... INFO @ Thu, 08 Oct 2020 19:49:53: end of X-cor INFO @ Thu, 08 Oct 2020 19:49:53: #2 finished! INFO @ Thu, 08 Oct 2020 19:49:53: #2 predicted fragment length is 2 bps INFO @ Thu, 08 Oct 2020 19:49:53: #2 alternative fragment length(s) may be 2,19,37 bps INFO @ Thu, 08 Oct 2020 19:49:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.10_model.r WARNING @ Thu, 08 Oct 2020 19:49:53: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:49:53: #2 You may need to consider one of the other alternative d(s): 2,19,37 WARNING @ Thu, 08 Oct 2020 19:49:53: #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 19:49:53: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:49:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:49:56: 17000000 INFO @ Thu, 08 Oct 2020 19:49:56: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:50:01: 18000000 INFO @ Thu, 08 Oct 2020 19:50:05: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:50:10: 20000000 INFO @ Thu, 08 Oct 2020 19:50:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:50:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:50:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.05_summits.bed INFO @ Thu, 08 Oct 2020 19:50:12: Done! INFO @ Thu, 08 Oct 2020 19:50:15: 21000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:50:20: 22000000 INFO @ Thu, 08 Oct 2020 19:50:24: #1 tag size is determined as 49 bps INFO @ Thu, 08 Oct 2020 19:50:24: #1 tag size = 49 INFO @ Thu, 08 Oct 2020 19:50:24: #1 total tags in treatment: 22750358 INFO @ Thu, 08 Oct 2020 19:50:24: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:50:24: #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 19:50:24: #1 tags after filtering in treatment: 22750358 INFO @ Thu, 08 Oct 2020 19:50:24: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:50:24: #1 finished! INFO @ Thu, 08 Oct 2020 19:50:24: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:50:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:50:25: #2 number of paired peaks: 405 WARNING @ Thu, 08 Oct 2020 19:50:25: Fewer paired peaks (405) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 405 pairs to build model! INFO @ Thu, 08 Oct 2020 19:50:25: start model_add_line... INFO @ Thu, 08 Oct 2020 19:50:26: start X-correlation... INFO @ Thu, 08 Oct 2020 19:50:26: end of X-cor INFO @ Thu, 08 Oct 2020 19:50:26: #2 finished! INFO @ Thu, 08 Oct 2020 19:50:26: #2 predicted fragment length is 2 bps INFO @ Thu, 08 Oct 2020 19:50:26: #2 alternative fragment length(s) may be 2,19,37 bps INFO @ Thu, 08 Oct 2020 19:50:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.20_model.r WARNING @ Thu, 08 Oct 2020 19:50:26: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 19:50:26: #2 You may need to consider one of the other alternative d(s): 2,19,37 WARNING @ Thu, 08 Oct 2020 19:50:26: #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 19:50:26: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:50:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:50:28: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:50:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:50:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:50:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.10_summits.bed INFO @ Thu, 08 Oct 2020 19:50:43: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:51:01: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:51:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:51:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:51:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6799190/SRX6799190.20_summits.bed INFO @ Thu, 08 Oct 2020 19:51:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling