Job ID = 6367897 SRX = SRX4194186 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:43:48 prefetch.2.10.7: 1) Downloading 'SRR7291445'... 2020-06-15T23:43:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:45:58 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:45:59 prefetch.2.10.7: 'SRR7291445' is valid 2020-06-15T23:45:59 prefetch.2.10.7: 1) 'SRR7291445' was downloaded successfully 2020-06-15T23:45:59 prefetch.2.10.7: 'SRR7291445' has 0 unresolved dependencies Read 5955677 spots for SRR7291445/SRR7291445.sra Written 5955677 spots for SRR7291445/SRR7291445.sra 2020-06-15T23:46:35 prefetch.2.10.7: 1) Downloading 'SRR7291446'... 2020-06-15T23:46:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:48:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:48:06 prefetch.2.10.7: 'SRR7291446' is valid 2020-06-15T23:48:06 prefetch.2.10.7: 1) 'SRR7291446' was downloaded successfully 2020-06-15T23:48:06 prefetch.2.10.7: 'SRR7291446' has 0 unresolved dependencies Read 5805692 spots for SRR7291446/SRR7291446.sra Written 5805692 spots for SRR7291446/SRR7291446.sra 2020-06-15T23:48:53 prefetch.2.10.7: 1) Downloading 'SRR7291447'... 2020-06-15T23:48:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:50 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:50 prefetch.2.10.7: 'SRR7291447' is valid 2020-06-15T23:49:50 prefetch.2.10.7: 1) 'SRR7291447' was downloaded successfully 2020-06-15T23:49:50 prefetch.2.10.7: 'SRR7291447' has 0 unresolved dependencies Read 5954642 spots for SRR7291447/SRR7291447.sra Written 5954642 spots for SRR7291447/SRR7291447.sra 2020-06-15T23:50:26 prefetch.2.10.7: 1) Downloading 'SRR7291448'... 2020-06-15T23:50:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:10 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:11 prefetch.2.10.7: 'SRR7291448' is valid 2020-06-15T23:51:11 prefetch.2.10.7: 1) 'SRR7291448' was downloaded successfully 2020-06-15T23:51:11 prefetch.2.10.7: 'SRR7291448' has 0 unresolved dependencies Read 5752810 spots for SRR7291448/SRR7291448.sra Written 5752810 spots for SRR7291448/SRR7291448.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: 00:11:21 23468821 reads; of these: 23468821 (100.00%) were unpaired; of these: 827972 (3.53%) aligned 0 times 15441899 (65.80%) aligned exactly 1 time 7198950 (30.67%) aligned >1 times 96.47% overall alignment rate Time searching: 00:11:21 Overall time: 00:11:21 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] 6351610 / 22640849 = 0.2805 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 09:10:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.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 09:10:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:27: 1000000 INFO @ Tue, 16 Jun 2020 09:10:34: 2000000 INFO @ Tue, 16 Jun 2020 09:10:41: 3000000 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 09:10:48: 4000000 INFO @ Tue, 16 Jun 2020 09:10:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.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 09:10:50: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:50: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:56: 5000000 INFO @ Tue, 16 Jun 2020 09:10:56: 1000000 INFO @ Tue, 16 Jun 2020 09:11:03: 2000000 INFO @ Tue, 16 Jun 2020 09:11:04: 6000000 INFO @ Tue, 16 Jun 2020 09:11:10: 3000000 INFO @ Tue, 16 Jun 2020 09:11:11: 7000000 INFO @ Tue, 16 Jun 2020 09:11:17: 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 09:11:19: 8000000 INFO @ Tue, 16 Jun 2020 09:11:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.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 09:11:20: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:20: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:23: 5000000 INFO @ Tue, 16 Jun 2020 09:11:26: 9000000 INFO @ Tue, 16 Jun 2020 09:11:27: 1000000 INFO @ Tue, 16 Jun 2020 09:11:30: 6000000 INFO @ Tue, 16 Jun 2020 09:11:34: 2000000 INFO @ Tue, 16 Jun 2020 09:11:34: 10000000 INFO @ Tue, 16 Jun 2020 09:11:37: 7000000 INFO @ Tue, 16 Jun 2020 09:11:41: 3000000 INFO @ Tue, 16 Jun 2020 09:11:42: 11000000 INFO @ Tue, 16 Jun 2020 09:11:45: 8000000 INFO @ Tue, 16 Jun 2020 09:11:48: 4000000 INFO @ Tue, 16 Jun 2020 09:11:49: 12000000 INFO @ Tue, 16 Jun 2020 09:11:52: 9000000 INFO @ Tue, 16 Jun 2020 09:11:55: 5000000 INFO @ Tue, 16 Jun 2020 09:11:57: 13000000 INFO @ Tue, 16 Jun 2020 09:11:59: 10000000 INFO @ Tue, 16 Jun 2020 09:12:02: 6000000 INFO @ Tue, 16 Jun 2020 09:12:05: 14000000 INFO @ Tue, 16 Jun 2020 09:12:06: 11000000 INFO @ Tue, 16 Jun 2020 09:12:09: 7000000 INFO @ Tue, 16 Jun 2020 09:12:12: 15000000 INFO @ Tue, 16 Jun 2020 09:12:13: 12000000 INFO @ Tue, 16 Jun 2020 09:12:16: 8000000 INFO @ Tue, 16 Jun 2020 09:12:20: 13000000 INFO @ Tue, 16 Jun 2020 09:12:20: 16000000 INFO @ Tue, 16 Jun 2020 09:12:23: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 09:12:23: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 09:12:23: #1 total tags in treatment: 16289239 INFO @ Tue, 16 Jun 2020 09:12:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:23: #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 09:12:23: #1 tags after filtering in treatment: 16289239 INFO @ Tue, 16 Jun 2020 09:12:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:23: 9000000 INFO @ Tue, 16 Jun 2020 09:12:24: #2 number of paired peaks: 1157 INFO @ Tue, 16 Jun 2020 09:12:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:24: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:12:24: #2 alternative fragment length(s) may be 1,53,69 bps INFO @ Tue, 16 Jun 2020 09:12:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.05_model.r WARNING @ Tue, 16 Jun 2020 09:12:24: #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 09:12:24: #2 You may need to consider one of the other alternative d(s): 1,53,69 WARNING @ Tue, 16 Jun 2020 09:12:24: #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 09:12:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:27: 14000000 INFO @ Tue, 16 Jun 2020 09:12:30: 10000000 INFO @ Tue, 16 Jun 2020 09:12:34: 15000000 INFO @ Tue, 16 Jun 2020 09:12:37: 11000000 INFO @ Tue, 16 Jun 2020 09:12:41: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:12:43: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 09:12:43: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 09:12:43: #1 total tags in treatment: 16289239 INFO @ Tue, 16 Jun 2020 09:12:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:43: #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 09:12:43: #1 tags after filtering in treatment: 16289239 INFO @ Tue, 16 Jun 2020 09:12:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:12:43: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:43: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:43: 12000000 INFO @ Tue, 16 Jun 2020 09:12:44: #2 number of paired peaks: 1157 INFO @ Tue, 16 Jun 2020 09:12:44: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:44: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:44: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:44: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:44: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:12:44: #2 alternative fragment length(s) may be 1,53,69 bps INFO @ Tue, 16 Jun 2020 09:12:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.10_model.r WARNING @ Tue, 16 Jun 2020 09:12:44: #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 09:12:44: #2 You may need to consider one of the other alternative d(s): 1,53,69 WARNING @ Tue, 16 Jun 2020 09:12:44: #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 09:12:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:50: 13000000 INFO @ Tue, 16 Jun 2020 09:12:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:56: 14000000 INFO @ Tue, 16 Jun 2020 09:13:02: 15000000 INFO @ Tue, 16 Jun 2020 09:13:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.05_summits.bed INFO @ Tue, 16 Jun 2020 09:13:04: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:13:09: 16000000 INFO @ Tue, 16 Jun 2020 09:13:11: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 09:13:11: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 09:13:11: #1 total tags in treatment: 16289239 INFO @ Tue, 16 Jun 2020 09:13:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:11: #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 09:13:11: #1 tags after filtering in treatment: 16289239 INFO @ Tue, 16 Jun 2020 09:13:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:13:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:12: #2 number of paired peaks: 1157 INFO @ Tue, 16 Jun 2020 09:13:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:12: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 09:13:12: #2 alternative fragment length(s) may be 1,53,69 bps INFO @ Tue, 16 Jun 2020 09:13:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.20_model.r WARNING @ Tue, 16 Jun 2020 09:13:12: #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 09:13:12: #2 You may need to consider one of the other alternative d(s): 1,53,69 WARNING @ Tue, 16 Jun 2020 09:13:12: #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 09:13:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:13:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.10_summits.bed INFO @ Tue, 16 Jun 2020 09:13:24: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:13:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194186/SRX4194186.20_summits.bed INFO @ Tue, 16 Jun 2020 09:13:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling