Job ID = 6368948 SRX = SRX7574652 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:35:50 prefetch.2.10.7: 1) Downloading 'SRR10906499'... 2020-06-16T00:35:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:39:08 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:39:09 prefetch.2.10.7: 'SRR10906499' is valid 2020-06-16T00:39:09 prefetch.2.10.7: 1) 'SRR10906499' was downloaded successfully 2020-06-16T00:39:09 prefetch.2.10.7: 'SRR10906499' has 0 unresolved dependencies Read 29603116 spots for SRR10906499/SRR10906499.sra Written 29603116 spots for SRR10906499/SRR10906499.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: 00:04:56 29603116 reads; of these: 29603116 (100.00%) were unpaired; of these: 13179499 (44.52%) aligned 0 times 13791032 (46.59%) aligned exactly 1 time 2632585 (8.89%) aligned >1 times 55.48% overall alignment rate Time searching: 00:04:56 Overall time: 00:04:56 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 8 files... [bam_rmdupse_core] 7413284 / 16423617 = 0.4514 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 09:48:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.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 09:48:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:36: 1000000 INFO @ Tue, 16 Jun 2020 09:48:42: 2000000 INFO @ Tue, 16 Jun 2020 09:48:49: 3000000 INFO @ Tue, 16 Jun 2020 09:48:55: 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 @ Tue, 16 Jun 2020 09:49:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.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 09:49:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:02: 5000000 INFO @ Tue, 16 Jun 2020 09:49:06: 1000000 INFO @ Tue, 16 Jun 2020 09:49:08: 6000000 INFO @ Tue, 16 Jun 2020 09:49:12: 2000000 INFO @ Tue, 16 Jun 2020 09:49:15: 7000000 INFO @ Tue, 16 Jun 2020 09:49:19: 3000000 INFO @ Tue, 16 Jun 2020 09:49:22: 8000000 INFO @ Tue, 16 Jun 2020 09:49:25: 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 @ Tue, 16 Jun 2020 09:49:29: 9000000 INFO @ Tue, 16 Jun 2020 09:49:29: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:49:29: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:49:29: #1 total tags in treatment: 9010333 INFO @ Tue, 16 Jun 2020 09:49:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:29: #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 09:49:29: #1 tags after filtering in treatment: 9010333 INFO @ Tue, 16 Jun 2020 09:49:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:29: #2 number of paired peaks: 362 WARNING @ Tue, 16 Jun 2020 09:49:29: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Tue, 16 Jun 2020 09:49:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:30: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:49:30: #2 alternative fragment length(s) may be 3,48,547 bps INFO @ Tue, 16 Jun 2020 09:49:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.05_model.r WARNING @ Tue, 16 Jun 2020 09:49:30: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:49:30: #2 You may need to consider one of the other alternative d(s): 3,48,547 WARNING @ Tue, 16 Jun 2020 09:49:30: #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 09:49:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.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 09:49:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:31: 5000000 INFO @ Tue, 16 Jun 2020 09:49:36: 1000000 INFO @ Tue, 16 Jun 2020 09:49:38: 6000000 INFO @ Tue, 16 Jun 2020 09:49:42: 2000000 INFO @ Tue, 16 Jun 2020 09:49:44: 7000000 INFO @ Tue, 16 Jun 2020 09:49:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:48: 3000000 INFO @ Tue, 16 Jun 2020 09:49:50: 8000000 INFO @ Tue, 16 Jun 2020 09:49:54: 4000000 INFO @ Tue, 16 Jun 2020 09:49:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.05_summits.bed INFO @ Tue, 16 Jun 2020 09:49:56: Done! INFO @ Tue, 16 Jun 2020 09:49:56: 9000000 pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (808 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:49:56: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:49:56: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:49:56: #1 total tags in treatment: 9010333 INFO @ Tue, 16 Jun 2020 09:49:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:56: #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 09:49:56: #1 tags after filtering in treatment: 9010333 INFO @ Tue, 16 Jun 2020 09:49:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:56: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:57: #2 number of paired peaks: 362 WARNING @ Tue, 16 Jun 2020 09:49:57: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Tue, 16 Jun 2020 09:49:57: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:57: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:57: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:57: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:57: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:49:57: #2 alternative fragment length(s) may be 3,48,547 bps INFO @ Tue, 16 Jun 2020 09:49:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.10_model.r WARNING @ Tue, 16 Jun 2020 09:49:57: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:49:57: #2 You may need to consider one of the other alternative d(s): 3,48,547 WARNING @ Tue, 16 Jun 2020 09:49:57: #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 09:49:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:50:00: 5000000 INFO @ Tue, 16 Jun 2020 09:50:06: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:50:11: 7000000 INFO @ Tue, 16 Jun 2020 09:50:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:17: 8000000 INFO @ Tue, 16 Jun 2020 09:50:22: 9000000 INFO @ Tue, 16 Jun 2020 09:50:23: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:50:23: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:50:23: #1 total tags in treatment: 9010333 INFO @ Tue, 16 Jun 2020 09:50:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:23: #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 09:50:23: #1 tags after filtering in treatment: 9010333 INFO @ Tue, 16 Jun 2020 09:50:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.10_summits.bed INFO @ Tue, 16 Jun 2020 09:50:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (533 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:50:23: #2 number of paired peaks: 362 WARNING @ Tue, 16 Jun 2020 09:50:23: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Tue, 16 Jun 2020 09:50:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:23: #2 predicted fragment length is 48 bps INFO @ Tue, 16 Jun 2020 09:50:23: #2 alternative fragment length(s) may be 3,48,547 bps INFO @ Tue, 16 Jun 2020 09:50:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.20_model.r WARNING @ Tue, 16 Jun 2020 09:50:23: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:50:23: #2 You may need to consider one of the other alternative d(s): 3,48,547 WARNING @ Tue, 16 Jun 2020 09:50:23: #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 09:50:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:50:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7574652/SRX7574652.20_summits.bed INFO @ Tue, 16 Jun 2020 09:50:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (254 records, 4 fields): 1 millis CompletedMACS2peakCalling