Job ID = 6497477 SRX = SRX494978 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:13:44 prefetch.2.10.7: 1) Downloading 'SRR1198510'... 2020-06-25T22:13:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:15:02 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:15:03 prefetch.2.10.7: 'SRR1198510' is valid 2020-06-25T22:15:03 prefetch.2.10.7: 1) 'SRR1198510' was downloaded successfully Read 16137366 spots for SRR1198510/SRR1198510.sra Written 16137366 spots for SRR1198510/SRR1198510.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: 00:00:01 Multiseed full-index search: 00:02:29 16137366 reads; of these: 16137366 (100.00%) were unpaired; of these: 923606 (5.72%) aligned 0 times 12431841 (77.04%) aligned exactly 1 time 2781919 (17.24%) aligned >1 times 94.28% overall alignment rate Time searching: 00:02:30 Overall time: 00:02:30 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] 1283519 / 15213760 = 0.0844 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 07:21:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.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 07:21:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:21:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:21:49: 1000000 INFO @ Fri, 26 Jun 2020 07:21:55: 2000000 INFO @ Fri, 26 Jun 2020 07:22:00: 3000000 INFO @ Fri, 26 Jun 2020 07:22:05: 4000000 INFO @ Fri, 26 Jun 2020 07:22:10: 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 @ Fri, 26 Jun 2020 07:22:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.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 07:22:15: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:22:15: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:22:15: 6000000 INFO @ Fri, 26 Jun 2020 07:22:20: 1000000 INFO @ Fri, 26 Jun 2020 07:22:21: 7000000 INFO @ Fri, 26 Jun 2020 07:22:26: 2000000 INFO @ Fri, 26 Jun 2020 07:22:26: 8000000 INFO @ Fri, 26 Jun 2020 07:22:31: 3000000 INFO @ Fri, 26 Jun 2020 07:22:32: 9000000 INFO @ Fri, 26 Jun 2020 07:22:37: 4000000 INFO @ Fri, 26 Jun 2020 07:22:37: 10000000 INFO @ Fri, 26 Jun 2020 07:22:42: 5000000 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 07:22:42: 11000000 INFO @ Fri, 26 Jun 2020 07:22:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.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 07:22:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:22:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:22:47: 6000000 INFO @ Fri, 26 Jun 2020 07:22:48: 12000000 INFO @ Fri, 26 Jun 2020 07:22:50: 1000000 INFO @ Fri, 26 Jun 2020 07:22:53: 7000000 INFO @ Fri, 26 Jun 2020 07:22:53: 13000000 INFO @ Fri, 26 Jun 2020 07:22:55: 2000000 INFO @ Fri, 26 Jun 2020 07:22:58: 8000000 INFO @ Fri, 26 Jun 2020 07:22:58: #1 tag size is determined as 28 bps INFO @ Fri, 26 Jun 2020 07:22:58: #1 tag size = 28 INFO @ Fri, 26 Jun 2020 07:22:58: #1 total tags in treatment: 13930241 INFO @ Fri, 26 Jun 2020 07:22:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:22:58: #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 07:22:58: #1 tags after filtering in treatment: 13930241 INFO @ Fri, 26 Jun 2020 07:22:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:22:58: #1 finished! INFO @ Fri, 26 Jun 2020 07:22:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:22:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:22:59: #2 number of paired peaks: 314 WARNING @ Fri, 26 Jun 2020 07:22:59: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Fri, 26 Jun 2020 07:22:59: start model_add_line... INFO @ Fri, 26 Jun 2020 07:22:59: start X-correlation... INFO @ Fri, 26 Jun 2020 07:23:00: end of X-cor INFO @ Fri, 26 Jun 2020 07:23:00: #2 finished! INFO @ Fri, 26 Jun 2020 07:23:00: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 07:23:00: #2 alternative fragment length(s) may be 2,27,572 bps INFO @ Fri, 26 Jun 2020 07:23:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.05_model.r INFO @ Fri, 26 Jun 2020 07:23:01: 3000000 INFO @ Fri, 26 Jun 2020 07:23:03: 9000000 INFO @ Fri, 26 Jun 2020 07:23:06: 4000000 INFO @ Fri, 26 Jun 2020 07:23:09: 10000000 INFO @ Fri, 26 Jun 2020 07:23:11: 5000000 INFO @ Fri, 26 Jun 2020 07:23:14: 11000000 WARNING @ Fri, 26 Jun 2020 07:23:14: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:23:14: #2 You may need to consider one of the other alternative d(s): 2,27,572 WARNING @ Fri, 26 Jun 2020 07:23:14: #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 07:23:14: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:23:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:23:17: 6000000 INFO @ Fri, 26 Jun 2020 07:23:19: 12000000 INFO @ Fri, 26 Jun 2020 07:23:22: 7000000 INFO @ Fri, 26 Jun 2020 07:23:25: 13000000 INFO @ Fri, 26 Jun 2020 07:23:28: 8000000 INFO @ Fri, 26 Jun 2020 07:23:29: #1 tag size is determined as 28 bps INFO @ Fri, 26 Jun 2020 07:23:29: #1 tag size = 28 INFO @ Fri, 26 Jun 2020 07:23:29: #1 total tags in treatment: 13930241 INFO @ Fri, 26 Jun 2020 07:23:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:23:29: #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 07:23:30: #1 tags after filtering in treatment: 13930241 INFO @ Fri, 26 Jun 2020 07:23:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:23:30: #1 finished! INFO @ Fri, 26 Jun 2020 07:23:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:23:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:23:31: #2 number of paired peaks: 314 WARNING @ Fri, 26 Jun 2020 07:23:31: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Fri, 26 Jun 2020 07:23:31: start model_add_line... INFO @ Fri, 26 Jun 2020 07:23:31: start X-correlation... INFO @ Fri, 26 Jun 2020 07:23:31: end of X-cor INFO @ Fri, 26 Jun 2020 07:23:31: #2 finished! INFO @ Fri, 26 Jun 2020 07:23:31: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 07:23:31: #2 alternative fragment length(s) may be 2,27,572 bps INFO @ Fri, 26 Jun 2020 07:23:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.10_model.r WARNING @ Fri, 26 Jun 2020 07:23:31: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:23:31: #2 You may need to consider one of the other alternative d(s): 2,27,572 WARNING @ Fri, 26 Jun 2020 07:23:31: #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 07:23:31: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:23:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:23:33: 9000000 INFO @ Fri, 26 Jun 2020 07:23:38: 10000000 INFO @ Fri, 26 Jun 2020 07:23:41: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:23:43: 11000000 INFO @ Fri, 26 Jun 2020 07:23:49: 12000000 INFO @ Fri, 26 Jun 2020 07:23:54: 13000000 INFO @ Fri, 26 Jun 2020 07:23:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.05_peaks.xls BedGraph に変換しました。 INFO @ Fri, 26 Jun 2020 07:23:57: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:23:58: #1 tag size is determined as 28 bps INFO @ Fri, 26 Jun 2020 07:23:58: #1 tag size = 28 INFO @ Fri, 26 Jun 2020 07:23:58: #1 total tags in treatment: 13930241 INFO @ Fri, 26 Jun 2020 07:23:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:23:58: #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 07:23:59: #1 tags after filtering in treatment: 13930241 INFO @ Fri, 26 Jun 2020 07:23:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:23:59: #1 finished! INFO @ Fri, 26 Jun 2020 07:23:59: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:23:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:24:00: #2 number of paired peaks: 314 WARNING @ Fri, 26 Jun 2020 07:24:00: Fewer paired peaks (314) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 314 pairs to build model! INFO @ Fri, 26 Jun 2020 07:24:00: start model_add_line... INFO @ Fri, 26 Jun 2020 07:24:00: start X-correlation... INFO @ Fri, 26 Jun 2020 07:24:00: end of X-cor INFO @ Fri, 26 Jun 2020 07:24:00: #2 finished! INFO @ Fri, 26 Jun 2020 07:24:00: #2 predicted fragment length is 2 bps INFO @ Fri, 26 Jun 2020 07:24:00: #2 alternative fragment length(s) may be 2,27,572 bps INFO @ Fri, 26 Jun 2020 07:24:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.20_model.r INFO @ Fri, 26 Jun 2020 07:24:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:24:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:24:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.05_summits.bed INFO @ Fri, 26 Jun 2020 07:24:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.10_peaks.narrowPeak WARNING @ Fri, 26 Jun 2020 07:24:43: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:24:43: #2 You may need to consider one of the other alternative d(s): 2,27,572 WARNING @ Fri, 26 Jun 2020 07:24:43: #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 07:24:43: Done! INFO @ Fri, 26 Jun 2020 07:24:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:24:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:24:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.10_summits.bed INFO @ Fri, 26 Jun 2020 07:24:43: Done! BigWig に変換中... pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:25:09: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:25:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:25:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:25:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494978/SRX494978.20_summits.bed INFO @ Fri, 26 Jun 2020 07:25:34: Done! BigWig に変換しました。 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling