Job ID = 6367704 SRX = SRX395528 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:32:20 prefetch.2.10.7: 1) Downloading 'SRR1054256'... 2020-06-15T23:32:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:33:22 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:33:22 prefetch.2.10.7: 'SRR1054256' is valid 2020-06-15T23:33:22 prefetch.2.10.7: 1) 'SRR1054256' was downloaded successfully Read 7590563 spots for SRR1054256/SRR1054256.sra Written 7590563 spots for SRR1054256/SRR1054256.sra 2020-06-15T23:33:52 prefetch.2.10.7: 1) Downloading 'SRR1054257'... 2020-06-15T23:33:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:35:11 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:35:12 prefetch.2.10.7: 'SRR1054257' is valid 2020-06-15T23:35:12 prefetch.2.10.7: 1) 'SRR1054257' was downloaded successfully Read 6200523 spots for SRR1054257/SRR1054257.sra Written 6200523 spots for SRR1054257/SRR1054257.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: 00:02:03 13791086 reads; of these: 13791086 (100.00%) were unpaired; of these: 867980 (6.29%) aligned 0 times 10870560 (78.82%) aligned exactly 1 time 2052546 (14.88%) aligned >1 times 93.71% overall alignment rate Time searching: 00:02:03 Overall time: 00:02:03 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_rmdupse_core] 1615331 / 12923106 = 0.1250 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 @ Tue, 16 Jun 2020 08:40:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.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 @ Tue, 16 Jun 2020 08:40:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:32: 1000000 INFO @ Tue, 16 Jun 2020 08:40:38: 2000000 INFO @ Tue, 16 Jun 2020 08:40:43: 3000000 INFO @ Tue, 16 Jun 2020 08:40:49: 4000000 INFO @ Tue, 16 Jun 2020 08:40:54: 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 @ Tue, 16 Jun 2020 08:40:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.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 @ Tue, 16 Jun 2020 08:40:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:40:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:59: 6000000 INFO @ Tue, 16 Jun 2020 08:41:02: 1000000 INFO @ Tue, 16 Jun 2020 08:41:05: 7000000 INFO @ Tue, 16 Jun 2020 08:41:08: 2000000 INFO @ Tue, 16 Jun 2020 08:41:11: 8000000 INFO @ Tue, 16 Jun 2020 08:41:14: 3000000 INFO @ Tue, 16 Jun 2020 08:41:16: 9000000 INFO @ Tue, 16 Jun 2020 08:41:20: 4000000 INFO @ Tue, 16 Jun 2020 08:41:22: 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 @ Tue, 16 Jun 2020 08:41:25: 5000000 INFO @ Tue, 16 Jun 2020 08:41:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.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 @ Tue, 16 Jun 2020 08:41:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:27: 11000000 INFO @ Tue, 16 Jun 2020 08:41:29: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:41:29: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:41:29: #1 total tags in treatment: 11307775 INFO @ Tue, 16 Jun 2020 08:41:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:41:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:41:29: #1 tags after filtering in treatment: 11307775 INFO @ Tue, 16 Jun 2020 08:41:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:41:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:41:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:41:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:41:30: #2 number of paired peaks: 278 WARNING @ Tue, 16 Jun 2020 08:41:30: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Tue, 16 Jun 2020 08:41:30: start model_add_line... INFO @ Tue, 16 Jun 2020 08:41:30: start X-correlation... INFO @ Tue, 16 Jun 2020 08:41:30: end of X-cor INFO @ Tue, 16 Jun 2020 08:41:30: #2 finished! INFO @ Tue, 16 Jun 2020 08:41:30: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:41:30: #2 alternative fragment length(s) may be 1,32,585 bps INFO @ Tue, 16 Jun 2020 08:41:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.05_model.r WARNING @ Tue, 16 Jun 2020 08:41:30: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:41:30: #2 You may need to consider one of the other alternative d(s): 1,32,585 WARNING @ Tue, 16 Jun 2020 08:41:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:41:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:41:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:41:31: 6000000 INFO @ Tue, 16 Jun 2020 08:41:32: 1000000 INFO @ Tue, 16 Jun 2020 08:41:36: 7000000 INFO @ Tue, 16 Jun 2020 08:41:37: 2000000 INFO @ Tue, 16 Jun 2020 08:41:42: 8000000 INFO @ Tue, 16 Jun 2020 08:41:42: 3000000 INFO @ Tue, 16 Jun 2020 08:41:47: 4000000 INFO @ Tue, 16 Jun 2020 08:41:48: 9000000 INFO @ Tue, 16 Jun 2020 08:41:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:41:52: 5000000 INFO @ Tue, 16 Jun 2020 08:41:53: 10000000 INFO @ Tue, 16 Jun 2020 08:41:58: 6000000 INFO @ Tue, 16 Jun 2020 08:41:59: 11000000 INFO @ Tue, 16 Jun 2020 08:42:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.05_summits.bed INFO @ Tue, 16 Jun 2020 08:42:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:42:01: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:42:01: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:42:01: #1 total tags in treatment: 11307775 INFO @ Tue, 16 Jun 2020 08:42:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:42:01: #1 tags after filtering in treatment: 11307775 INFO @ Tue, 16 Jun 2020 08:42:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:42:02: #2 number of paired peaks: 278 WARNING @ Tue, 16 Jun 2020 08:42:02: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Tue, 16 Jun 2020 08:42:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:02: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:42:02: #2 alternative fragment length(s) may be 1,32,585 bps INFO @ Tue, 16 Jun 2020 08:42:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.10_model.r WARNING @ Tue, 16 Jun 2020 08:42:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:42:02: #2 You may need to consider one of the other alternative d(s): 1,32,585 WARNING @ Tue, 16 Jun 2020 08:42:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:42:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:42:03: 7000000 INFO @ Tue, 16 Jun 2020 08:42:07: 8000000 INFO @ Tue, 16 Jun 2020 08:42:12: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:42:17: 10000000 INFO @ Tue, 16 Jun 2020 08:42:22: 11000000 INFO @ Tue, 16 Jun 2020 08:42:23: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 08:42:23: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 08:42:23: #1 total tags in treatment: 11307775 INFO @ Tue, 16 Jun 2020 08:42:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:42:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:42:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:23: #1 tags after filtering in treatment: 11307775 INFO @ Tue, 16 Jun 2020 08:42:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:42:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:42:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:42:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:42:24: #2 number of paired peaks: 278 WARNING @ Tue, 16 Jun 2020 08:42:24: Fewer paired peaks (278) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 278 pairs to build model! INFO @ Tue, 16 Jun 2020 08:42:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:42:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:42:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:42:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:42:24: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:42:24: #2 alternative fragment length(s) may be 1,32,585 bps INFO @ Tue, 16 Jun 2020 08:42:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.20_model.r WARNING @ Tue, 16 Jun 2020 08:42:24: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:42:24: #2 You may need to consider one of the other alternative d(s): 1,32,585 WARNING @ Tue, 16 Jun 2020 08:42:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:42:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:42:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:42:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.10_summits.bed INFO @ Tue, 16 Jun 2020 08:42:33: 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 @ Tue, 16 Jun 2020 08:42:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:42:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:42:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:42:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX395528/SRX395528.20_summits.bed INFO @ Tue, 16 Jun 2020 08:42:55: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling