Job ID = 10165782 SRX = SRX9120615 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 22488133 spots for SRR12638558/SRR12638558.sra Written 22488133 spots for SRR12638558/SRR12638558.sra fastq に変換しました。 bowtie でマッピング中... Your job 10166077 ("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: 00:04:43 22488133 reads; of these: 22488133 (100.00%) were unpaired; of these: 712842 (3.17%) aligned 0 times 18190771 (80.89%) aligned exactly 1 time 3584520 (15.94%) aligned >1 times 96.83% overall alignment rate Time searching: 00:04:43 Overall time: 00:04:43 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] 3064566 / 21775291 = 0.1407 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 20:01:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.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 20:01:49: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:01:49: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:01:54: 1000000 INFO @ Thu, 08 Oct 2020 20:02:00: 2000000 INFO @ Thu, 08 Oct 2020 20:02:05: 3000000 INFO @ Thu, 08 Oct 2020 20:02:11: 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 20:02:16: 5000000 INFO @ Thu, 08 Oct 2020 20:02:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.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 20:02:19: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:02:19: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:02:22: 6000000 INFO @ Thu, 08 Oct 2020 20:02:25: 1000000 INFO @ Thu, 08 Oct 2020 20:02:28: 7000000 INFO @ Thu, 08 Oct 2020 20:02:32: 2000000 INFO @ Thu, 08 Oct 2020 20:02:34: 8000000 INFO @ Thu, 08 Oct 2020 20:02:38: 3000000 INFO @ Thu, 08 Oct 2020 20:02:41: 9000000 INFO @ Thu, 08 Oct 2020 20:02:45: 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 20:02:47: 10000000 INFO @ Thu, 08 Oct 2020 20:02:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.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 20:02:49: #1 read tag files... INFO @ Thu, 08 Oct 2020 20:02:49: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 20:02:51: 5000000 INFO @ Thu, 08 Oct 2020 20:02:54: 11000000 INFO @ Thu, 08 Oct 2020 20:02:56: 1000000 INFO @ Thu, 08 Oct 2020 20:02:58: 6000000 INFO @ Thu, 08 Oct 2020 20:03:00: 12000000 INFO @ Thu, 08 Oct 2020 20:03:03: 2000000 INFO @ Thu, 08 Oct 2020 20:03:05: 7000000 INFO @ Thu, 08 Oct 2020 20:03:06: 13000000 INFO @ Thu, 08 Oct 2020 20:03:09: 3000000 INFO @ Thu, 08 Oct 2020 20:03:11: 8000000 INFO @ Thu, 08 Oct 2020 20:03:12: 14000000 INFO @ Thu, 08 Oct 2020 20:03:16: 4000000 INFO @ Thu, 08 Oct 2020 20:03:18: 9000000 INFO @ Thu, 08 Oct 2020 20:03:19: 15000000 INFO @ Thu, 08 Oct 2020 20:03:23: 5000000 INFO @ Thu, 08 Oct 2020 20:03:25: 10000000 INFO @ Thu, 08 Oct 2020 20:03:25: 16000000 INFO @ Thu, 08 Oct 2020 20:03:29: 6000000 INFO @ Thu, 08 Oct 2020 20:03:31: 17000000 INFO @ Thu, 08 Oct 2020 20:03:31: 11000000 INFO @ Thu, 08 Oct 2020 20:03:36: 7000000 INFO @ Thu, 08 Oct 2020 20:03:38: 18000000 INFO @ Thu, 08 Oct 2020 20:03:38: 12000000 INFO @ Thu, 08 Oct 2020 20:03:42: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:03:42: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:03:42: #1 total tags in treatment: 18710725 INFO @ Thu, 08 Oct 2020 20:03:42: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:03:42: #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 20:03:43: 8000000 INFO @ Thu, 08 Oct 2020 20:03:43: #1 tags after filtering in treatment: 18710725 INFO @ Thu, 08 Oct 2020 20:03:43: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:03:43: #1 finished! INFO @ Thu, 08 Oct 2020 20:03:43: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:03:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:03:44: #2 number of paired peaks: 202 WARNING @ Thu, 08 Oct 2020 20:03:44: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Thu, 08 Oct 2020 20:03:44: start model_add_line... INFO @ Thu, 08 Oct 2020 20:03:44: start X-correlation... INFO @ Thu, 08 Oct 2020 20:03:44: end of X-cor INFO @ Thu, 08 Oct 2020 20:03:44: #2 finished! INFO @ Thu, 08 Oct 2020 20:03:44: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:03:44: #2 alternative fragment length(s) may be 1,46,531 bps INFO @ Thu, 08 Oct 2020 20:03:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.05_model.r WARNING @ Thu, 08 Oct 2020 20:03:44: #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 20:03:44: #2 You may need to consider one of the other alternative d(s): 1,46,531 WARNING @ Thu, 08 Oct 2020 20:03:44: #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 20:03:44: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:03:44: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:03:45: 13000000 INFO @ Thu, 08 Oct 2020 20:03:49: 9000000 INFO @ Thu, 08 Oct 2020 20:03:51: 14000000 INFO @ Thu, 08 Oct 2020 20:03:56: 10000000 INFO @ Thu, 08 Oct 2020 20:03:58: 15000000 INFO @ Thu, 08 Oct 2020 20:04:02: 11000000 INFO @ Thu, 08 Oct 2020 20:04:04: 16000000 INFO @ Thu, 08 Oct 2020 20:04:09: 12000000 INFO @ Thu, 08 Oct 2020 20:04:11: 17000000 INFO @ Thu, 08 Oct 2020 20:04:15: 13000000 INFO @ Thu, 08 Oct 2020 20:04:17: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:04:17: 18000000 INFO @ Thu, 08 Oct 2020 20:04:22: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:04:22: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:04:22: #1 total tags in treatment: 18710725 INFO @ Thu, 08 Oct 2020 20:04:22: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:04:22: #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 20:04:22: 14000000 INFO @ Thu, 08 Oct 2020 20:04:22: #1 tags after filtering in treatment: 18710725 INFO @ Thu, 08 Oct 2020 20:04:22: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:04:22: #1 finished! INFO @ Thu, 08 Oct 2020 20:04:22: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:04:22: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:04:23: #2 number of paired peaks: 202 WARNING @ Thu, 08 Oct 2020 20:04:23: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Thu, 08 Oct 2020 20:04:23: start model_add_line... INFO @ Thu, 08 Oct 2020 20:04:23: start X-correlation... INFO @ Thu, 08 Oct 2020 20:04:23: end of X-cor INFO @ Thu, 08 Oct 2020 20:04:23: #2 finished! INFO @ Thu, 08 Oct 2020 20:04:23: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:04:23: #2 alternative fragment length(s) may be 1,46,531 bps INFO @ Thu, 08 Oct 2020 20:04:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.10_model.r WARNING @ Thu, 08 Oct 2020 20:04:23: #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 20:04:23: #2 You may need to consider one of the other alternative d(s): 1,46,531 WARNING @ Thu, 08 Oct 2020 20:04:23: #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 20:04:23: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:04:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:04:28: 15000000 INFO @ Thu, 08 Oct 2020 20:04:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.05_peaks.xls INFO @ Thu, 08 Oct 2020 20:04:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:04:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.05_summits.bed INFO @ Thu, 08 Oct 2020 20:04:33: Done! BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 20:04:34: 16000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 20:04:40: 17000000 INFO @ Thu, 08 Oct 2020 20:04:46: 18000000 INFO @ Thu, 08 Oct 2020 20:04:50: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 20:04:50: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 20:04:50: #1 total tags in treatment: 18710725 INFO @ Thu, 08 Oct 2020 20:04:50: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 20:04:50: #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 20:04:51: #1 tags after filtering in treatment: 18710725 INFO @ Thu, 08 Oct 2020 20:04:51: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 20:04:51: #1 finished! INFO @ Thu, 08 Oct 2020 20:04:51: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 20:04:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 20:04:52: #2 number of paired peaks: 202 WARNING @ Thu, 08 Oct 2020 20:04:52: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Thu, 08 Oct 2020 20:04:52: start model_add_line... INFO @ Thu, 08 Oct 2020 20:04:52: start X-correlation... INFO @ Thu, 08 Oct 2020 20:04:52: end of X-cor INFO @ Thu, 08 Oct 2020 20:04:52: #2 finished! INFO @ Thu, 08 Oct 2020 20:04:52: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 20:04:52: #2 alternative fragment length(s) may be 1,46,531 bps INFO @ Thu, 08 Oct 2020 20:04:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.20_model.r WARNING @ Thu, 08 Oct 2020 20:04:52: #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 20:04:52: #2 You may need to consider one of the other alternative d(s): 1,46,531 WARNING @ Thu, 08 Oct 2020 20:04:52: #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 20:04:52: #3 Call peaks... INFO @ Thu, 08 Oct 2020 20:04:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 20:04:52: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:05:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.10_peaks.xls INFO @ Thu, 08 Oct 2020 20:05:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:05:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.10_summits.bed INFO @ Thu, 08 Oct 2020 20:05:06: 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 20:05:22: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 20:05:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.20_peaks.xls INFO @ Thu, 08 Oct 2020 20:05:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 20:05:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9120615/SRX9120615.20_summits.bed INFO @ Thu, 08 Oct 2020 20:05:37: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling