Job ID = 6497365 SRX = SRX277030 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:12:03 prefetch.2.10.7: 1) Downloading 'SRR849699'... 2020-06-25T21:12:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:12:33 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:12:33 prefetch.2.10.7: 'SRR849699' is valid 2020-06-25T21:12:33 prefetch.2.10.7: 1) 'SRR849699' was downloaded successfully Read 3398916 spots for SRR849699/SRR849699.sra Written 3398916 spots for SRR849699/SRR849699.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: 00:00:31 3398916 reads; of these: 3398916 (100.00%) were unpaired; of these: 488066 (14.36%) aligned 0 times 2406258 (70.79%) aligned exactly 1 time 504592 (14.85%) aligned >1 times 85.64% overall alignment rate Time searching: 00:00:31 Overall time: 00:00:32 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] 130974 / 2910850 = 0.0450 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 06:14:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.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 06:14:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:14:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:14:24: 1000000 INFO @ Fri, 26 Jun 2020 06:14:30: 2000000 INFO @ Fri, 26 Jun 2020 06:14:35: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 06:14:35: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 06:14:35: #1 total tags in treatment: 2779876 INFO @ Fri, 26 Jun 2020 06:14:35: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:14:35: #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 06:14:35: #1 tags after filtering in treatment: 2779876 INFO @ Fri, 26 Jun 2020 06:14:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:14:35: #1 finished! INFO @ Fri, 26 Jun 2020 06:14:35: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:14:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:14:35: #2 number of paired peaks: 380 WARNING @ Fri, 26 Jun 2020 06:14:35: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Fri, 26 Jun 2020 06:14:35: start model_add_line... INFO @ Fri, 26 Jun 2020 06:14:35: start X-correlation... INFO @ Fri, 26 Jun 2020 06:14:35: end of X-cor INFO @ Fri, 26 Jun 2020 06:14:35: #2 finished! INFO @ Fri, 26 Jun 2020 06:14:35: #2 predicted fragment length is 36 bps INFO @ Fri, 26 Jun 2020 06:14:35: #2 alternative fragment length(s) may be 4,36,489,544,546,583 bps INFO @ Fri, 26 Jun 2020 06:14:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.05_model.r WARNING @ Fri, 26 Jun 2020 06:14:35: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:14:35: #2 You may need to consider one of the other alternative d(s): 4,36,489,544,546,583 WARNING @ Fri, 26 Jun 2020 06:14:35: #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 06:14:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:14:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:14:41: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:14:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.05_peaks.xls INFO @ Fri, 26 Jun 2020 06:14:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:14:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.05_summits.bed INFO @ Fri, 26 Jun 2020 06:14:44: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (276 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 06:14:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.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 06:14:48: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:14:48: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:14:54: 1000000 INFO @ Fri, 26 Jun 2020 06:14:59: 2000000 INFO @ Fri, 26 Jun 2020 06:15:03: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 06:15:03: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 06:15:03: #1 total tags in treatment: 2779876 INFO @ Fri, 26 Jun 2020 06:15:03: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:15:03: #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 06:15:03: #1 tags after filtering in treatment: 2779876 INFO @ Fri, 26 Jun 2020 06:15:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:15:03: #1 finished! INFO @ Fri, 26 Jun 2020 06:15:03: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:15:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:15:03: #2 number of paired peaks: 380 WARNING @ Fri, 26 Jun 2020 06:15:03: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Fri, 26 Jun 2020 06:15:03: start model_add_line... INFO @ Fri, 26 Jun 2020 06:15:03: start X-correlation... INFO @ Fri, 26 Jun 2020 06:15:03: end of X-cor INFO @ Fri, 26 Jun 2020 06:15:03: #2 finished! INFO @ Fri, 26 Jun 2020 06:15:03: #2 predicted fragment length is 36 bps INFO @ Fri, 26 Jun 2020 06:15:03: #2 alternative fragment length(s) may be 4,36,489,544,546,583 bps INFO @ Fri, 26 Jun 2020 06:15:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.10_model.r WARNING @ Fri, 26 Jun 2020 06:15:03: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:15:03: #2 You may need to consider one of the other alternative d(s): 4,36,489,544,546,583 WARNING @ Fri, 26 Jun 2020 06:15:03: #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 06:15:03: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:15:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 06:15:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:15:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.10_peaks.xls INFO @ Fri, 26 Jun 2020 06:15:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:15:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.10_summits.bed INFO @ Fri, 26 Jun 2020 06:15:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (111 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 06:15:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.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 06:15:18: #1 read tag files... INFO @ Fri, 26 Jun 2020 06:15:18: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 06:15:24: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 06:15:29: 2000000 INFO @ Fri, 26 Jun 2020 06:15:33: #1 tag size is determined as 32 bps INFO @ Fri, 26 Jun 2020 06:15:33: #1 tag size = 32 INFO @ Fri, 26 Jun 2020 06:15:33: #1 total tags in treatment: 2779876 INFO @ Fri, 26 Jun 2020 06:15:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 06:15:33: #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 06:15:33: #1 tags after filtering in treatment: 2779876 INFO @ Fri, 26 Jun 2020 06:15:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 06:15:33: #1 finished! INFO @ Fri, 26 Jun 2020 06:15:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 06:15:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 06:15:34: #2 number of paired peaks: 380 WARNING @ Fri, 26 Jun 2020 06:15:34: Fewer paired peaks (380) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 380 pairs to build model! INFO @ Fri, 26 Jun 2020 06:15:34: start model_add_line... INFO @ Fri, 26 Jun 2020 06:15:34: start X-correlation... INFO @ Fri, 26 Jun 2020 06:15:34: end of X-cor INFO @ Fri, 26 Jun 2020 06:15:34: #2 finished! INFO @ Fri, 26 Jun 2020 06:15:34: #2 predicted fragment length is 36 bps INFO @ Fri, 26 Jun 2020 06:15:34: #2 alternative fragment length(s) may be 4,36,489,544,546,583 bps INFO @ Fri, 26 Jun 2020 06:15:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.20_model.r WARNING @ Fri, 26 Jun 2020 06:15:34: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 06:15:34: #2 You may need to consider one of the other alternative d(s): 4,36,489,544,546,583 WARNING @ Fri, 26 Jun 2020 06:15:34: #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 06:15:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 06:15:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 06:15:40: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 06:15:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.20_peaks.xls INFO @ Fri, 26 Jun 2020 06:15:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 06:15:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277030/SRX277030.20_summits.bed INFO @ Fri, 26 Jun 2020 06:15:43: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (36 records, 4 fields): 2 millis CompletedMACS2peakCalling