Job ID = 6507931 SRX = SRX495025 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:43:31 prefetch.2.10.7: 1) Downloading 'SRR1198557'... 2020-06-26T13:43:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:45:46 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:45:46 prefetch.2.10.7: 1) 'SRR1198557' was downloaded successfully Read 22970231 spots for SRR1198557/SRR1198557.sra Written 22970231 spots for SRR1198557/SRR1198557.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:14 22970231 reads; of these: 22970231 (100.00%) were unpaired; of these: 2517065 (10.96%) aligned 0 times 16806167 (73.16%) aligned exactly 1 time 3646999 (15.88%) aligned >1 times 89.04% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 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] 2296920 / 20453166 = 0.1123 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 @ Fri, 26 Jun 2020 22:57:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.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 @ Fri, 26 Jun 2020 22:57:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:57:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:57:50: 1000000 INFO @ Fri, 26 Jun 2020 22:57:55: 2000000 INFO @ Fri, 26 Jun 2020 22:58:01: 3000000 INFO @ Fri, 26 Jun 2020 22:58:06: 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 @ Fri, 26 Jun 2020 22:58:12: 5000000 INFO @ Fri, 26 Jun 2020 22:58:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.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 @ Fri, 26 Jun 2020 22:58:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:58:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:58:18: 6000000 INFO @ Fri, 26 Jun 2020 22:58:20: 1000000 INFO @ Fri, 26 Jun 2020 22:58:23: 7000000 INFO @ Fri, 26 Jun 2020 22:58:26: 2000000 INFO @ Fri, 26 Jun 2020 22:58:29: 8000000 INFO @ Fri, 26 Jun 2020 22:58:31: 3000000 INFO @ Fri, 26 Jun 2020 22:58:35: 9000000 INFO @ Fri, 26 Jun 2020 22:58:37: 4000000 INFO @ Fri, 26 Jun 2020 22:58:40: 10000000 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 @ Fri, 26 Jun 2020 22:58:43: 5000000 INFO @ Fri, 26 Jun 2020 22:58:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.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 @ Fri, 26 Jun 2020 22:58:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:58:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:58:46: 11000000 INFO @ Fri, 26 Jun 2020 22:58:49: 6000000 INFO @ Fri, 26 Jun 2020 22:58:50: 1000000 INFO @ Fri, 26 Jun 2020 22:58:51: 12000000 INFO @ Fri, 26 Jun 2020 22:58:54: 7000000 INFO @ Fri, 26 Jun 2020 22:58:56: 2000000 INFO @ Fri, 26 Jun 2020 22:58:57: 13000000 INFO @ Fri, 26 Jun 2020 22:59:00: 8000000 INFO @ Fri, 26 Jun 2020 22:59:02: 3000000 INFO @ Fri, 26 Jun 2020 22:59:03: 14000000 INFO @ Fri, 26 Jun 2020 22:59:06: 9000000 INFO @ Fri, 26 Jun 2020 22:59:07: 4000000 INFO @ Fri, 26 Jun 2020 22:59:08: 15000000 INFO @ Fri, 26 Jun 2020 22:59:11: 10000000 INFO @ Fri, 26 Jun 2020 22:59:13: 5000000 INFO @ Fri, 26 Jun 2020 22:59:14: 16000000 INFO @ Fri, 26 Jun 2020 22:59:17: 11000000 INFO @ Fri, 26 Jun 2020 22:59:19: 17000000 INFO @ Fri, 26 Jun 2020 22:59:19: 6000000 INFO @ Fri, 26 Jun 2020 22:59:23: 12000000 INFO @ Fri, 26 Jun 2020 22:59:25: 18000000 INFO @ Fri, 26 Jun 2020 22:59:25: 7000000 INFO @ Fri, 26 Jun 2020 22:59:26: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:59:26: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:59:26: #1 total tags in treatment: 18156246 INFO @ Fri, 26 Jun 2020 22:59:26: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:59:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:59:26: #1 tags after filtering in treatment: 18156246 INFO @ Fri, 26 Jun 2020 22:59:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:59:26: #1 finished! INFO @ Fri, 26 Jun 2020 22:59:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:59:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:59:27: #2 number of paired peaks: 260 WARNING @ Fri, 26 Jun 2020 22:59:27: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Fri, 26 Jun 2020 22:59:27: start model_add_line... INFO @ Fri, 26 Jun 2020 22:59:27: start X-correlation... INFO @ Fri, 26 Jun 2020 22:59:27: end of X-cor INFO @ Fri, 26 Jun 2020 22:59:27: #2 finished! INFO @ Fri, 26 Jun 2020 22:59:27: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:59:27: #2 alternative fragment length(s) may be 1,31,572,593 bps INFO @ Fri, 26 Jun 2020 22:59:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.05_model.r WARNING @ Fri, 26 Jun 2020 22:59:27: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:59:27: #2 You may need to consider one of the other alternative d(s): 1,31,572,593 WARNING @ Fri, 26 Jun 2020 22:59:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:59:27: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:59:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:59:28: 13000000 INFO @ Fri, 26 Jun 2020 22:59:31: 8000000 INFO @ Fri, 26 Jun 2020 22:59:34: 14000000 INFO @ Fri, 26 Jun 2020 22:59:37: 9000000 INFO @ Fri, 26 Jun 2020 22:59:39: 15000000 INFO @ Fri, 26 Jun 2020 22:59:42: 10000000 INFO @ Fri, 26 Jun 2020 22:59:45: 16000000 INFO @ Fri, 26 Jun 2020 22:59:48: 11000000 INFO @ Fri, 26 Jun 2020 22:59:50: 17000000 INFO @ Fri, 26 Jun 2020 22:59:54: 12000000 INFO @ Fri, 26 Jun 2020 22:59:56: 18000000 INFO @ Fri, 26 Jun 2020 22:59:57: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:59:57: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:59:57: #1 total tags in treatment: 18156246 INFO @ Fri, 26 Jun 2020 22:59:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:59:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:59:57: #1 tags after filtering in treatment: 18156246 INFO @ Fri, 26 Jun 2020 22:59:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:59:57: #1 finished! INFO @ Fri, 26 Jun 2020 22:59:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:59:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:59:58: #2 number of paired peaks: 260 WARNING @ Fri, 26 Jun 2020 22:59:58: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Fri, 26 Jun 2020 22:59:58: start model_add_line... INFO @ Fri, 26 Jun 2020 22:59:59: start X-correlation... INFO @ Fri, 26 Jun 2020 22:59:59: end of X-cor INFO @ Fri, 26 Jun 2020 22:59:59: #2 finished! INFO @ Fri, 26 Jun 2020 22:59:59: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 22:59:59: #2 alternative fragment length(s) may be 1,31,572,593 bps INFO @ Fri, 26 Jun 2020 22:59:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.10_model.r WARNING @ Fri, 26 Jun 2020 22:59:59: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:59:59: #2 You may need to consider one of the other alternative d(s): 1,31,572,593 WARNING @ Fri, 26 Jun 2020 22:59:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:59:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:59:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:00:00: 13000000 INFO @ Fri, 26 Jun 2020 23:00:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:00:05: 14000000 INFO @ Fri, 26 Jun 2020 23:00:11: 15000000 INFO @ Fri, 26 Jun 2020 23:00:16: 16000000 INFO @ Fri, 26 Jun 2020 23:00:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:00:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:00:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.05_summits.bed INFO @ Fri, 26 Jun 2020 23:00:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:00:22: 17000000 INFO @ Fri, 26 Jun 2020 23:00:27: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:00:28: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:00:28: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:00:28: #1 total tags in treatment: 18156246 INFO @ Fri, 26 Jun 2020 23:00:28: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:00:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:00:28: #1 tags after filtering in treatment: 18156246 INFO @ Fri, 26 Jun 2020 23:00:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:00:28: #1 finished! INFO @ Fri, 26 Jun 2020 23:00:28: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:00:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:00:30: #2 number of paired peaks: 260 WARNING @ Fri, 26 Jun 2020 23:00:30: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Fri, 26 Jun 2020 23:00:30: start model_add_line... INFO @ Fri, 26 Jun 2020 23:00:30: start X-correlation... INFO @ Fri, 26 Jun 2020 23:00:30: end of X-cor INFO @ Fri, 26 Jun 2020 23:00:30: #2 finished! INFO @ Fri, 26 Jun 2020 23:00:30: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:00:30: #2 alternative fragment length(s) may be 1,31,572,593 bps INFO @ Fri, 26 Jun 2020 23:00:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.20_model.r WARNING @ Fri, 26 Jun 2020 23:00:30: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:00:30: #2 You may need to consider one of the other alternative d(s): 1,31,572,593 WARNING @ Fri, 26 Jun 2020 23:00:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:00:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:00:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:00:33: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:00:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:00:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:00:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.10_summits.bed INFO @ Fri, 26 Jun 2020 23:00:48: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:01:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:01:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:01:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:01:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495025/SRX495025.20_summits.bed INFO @ Fri, 26 Jun 2020 23:01:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling