Job ID = 6367026 SRX = SRX2710287 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:05:23 prefetch.2.10.7: 1) Downloading 'SRR5418741'... 2020-06-15T23:05:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:11:03 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:11:03 prefetch.2.10.7: 1) 'SRR5418741' was downloaded successfully Read 40067033 spots for SRR5418741/SRR5418741.sra Written 40067033 spots for SRR5418741/SRR5418741.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: 00:22:27 40067033 reads; of these: 40067033 (100.00%) were unpaired; of these: 3568901 (8.91%) aligned 0 times 18496793 (46.16%) aligned exactly 1 time 18001339 (44.93%) aligned >1 times 91.09% overall alignment rate Time searching: 00:22:27 Overall time: 00:22:27 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 16 files... [bam_rmdupse_core] 17950231 / 36498132 = 0.4918 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 08:48:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.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 08:48:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:14: 1000000 INFO @ Tue, 16 Jun 2020 08:48:21: 2000000 INFO @ Tue, 16 Jun 2020 08:48:28: 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 08:48:36: 4000000 INFO @ Tue, 16 Jun 2020 08:48:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.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 08:48:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:43: 5000000 INFO @ Tue, 16 Jun 2020 08:48:44: 1000000 INFO @ Tue, 16 Jun 2020 08:48:51: 6000000 INFO @ Tue, 16 Jun 2020 08:48:51: 2000000 INFO @ Tue, 16 Jun 2020 08:48:58: 3000000 INFO @ Tue, 16 Jun 2020 08:48:59: 7000000 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 08:49:06: 4000000 INFO @ Tue, 16 Jun 2020 08:49:06: 8000000 INFO @ Tue, 16 Jun 2020 08:49:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.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 08:49:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:13: 5000000 INFO @ Tue, 16 Jun 2020 08:49:15: 9000000 INFO @ Tue, 16 Jun 2020 08:49:15: 1000000 INFO @ Tue, 16 Jun 2020 08:49:20: 6000000 INFO @ Tue, 16 Jun 2020 08:49:23: 2000000 INFO @ Tue, 16 Jun 2020 08:49:23: 10000000 INFO @ Tue, 16 Jun 2020 08:49:27: 7000000 INFO @ Tue, 16 Jun 2020 08:49:32: 3000000 INFO @ Tue, 16 Jun 2020 08:49:32: 11000000 INFO @ Tue, 16 Jun 2020 08:49:34: 8000000 INFO @ Tue, 16 Jun 2020 08:49:41: 4000000 INFO @ Tue, 16 Jun 2020 08:49:41: 12000000 INFO @ Tue, 16 Jun 2020 08:49:41: 9000000 INFO @ Tue, 16 Jun 2020 08:49:49: 10000000 INFO @ Tue, 16 Jun 2020 08:49:49: 5000000 INFO @ Tue, 16 Jun 2020 08:49:49: 13000000 INFO @ Tue, 16 Jun 2020 08:49:56: 11000000 INFO @ Tue, 16 Jun 2020 08:49:58: 6000000 INFO @ Tue, 16 Jun 2020 08:49:58: 14000000 INFO @ Tue, 16 Jun 2020 08:50:03: 12000000 INFO @ Tue, 16 Jun 2020 08:50:07: 7000000 INFO @ Tue, 16 Jun 2020 08:50:07: 15000000 INFO @ Tue, 16 Jun 2020 08:50:10: 13000000 INFO @ Tue, 16 Jun 2020 08:50:15: 8000000 INFO @ Tue, 16 Jun 2020 08:50:15: 16000000 INFO @ Tue, 16 Jun 2020 08:50:17: 14000000 INFO @ Tue, 16 Jun 2020 08:50:24: 9000000 INFO @ Tue, 16 Jun 2020 08:50:24: 17000000 INFO @ Tue, 16 Jun 2020 08:50:25: 15000000 INFO @ Tue, 16 Jun 2020 08:50:32: 16000000 INFO @ Tue, 16 Jun 2020 08:50:32: 10000000 INFO @ Tue, 16 Jun 2020 08:50:32: 18000000 INFO @ Tue, 16 Jun 2020 08:50:37: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:50:37: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:50:37: #1 total tags in treatment: 18547901 INFO @ Tue, 16 Jun 2020 08:50:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:37: #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 08:50:37: #1 tags after filtering in treatment: 18547901 INFO @ Tue, 16 Jun 2020 08:50:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:50:39: #2 number of paired peaks: 1017 INFO @ Tue, 16 Jun 2020 08:50:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:39: 17000000 INFO @ Tue, 16 Jun 2020 08:50:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:39: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:50:39: #2 alternative fragment length(s) may be 1,67 bps INFO @ Tue, 16 Jun 2020 08:50:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.05_model.r WARNING @ Tue, 16 Jun 2020 08:50:39: #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 08:50:39: #2 You may need to consider one of the other alternative d(s): 1,67 WARNING @ Tue, 16 Jun 2020 08:50:39: #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 08:50:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:40: 11000000 INFO @ Tue, 16 Jun 2020 08:50:46: 18000000 INFO @ Tue, 16 Jun 2020 08:50:48: 12000000 INFO @ Tue, 16 Jun 2020 08:50:50: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:50:50: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:50:50: #1 total tags in treatment: 18547901 INFO @ Tue, 16 Jun 2020 08:50:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:50:50: #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 08:50:50: #1 tags after filtering in treatment: 18547901 INFO @ Tue, 16 Jun 2020 08:50:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:50:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:50:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:50:50: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:50:52: #2 number of paired peaks: 1017 INFO @ Tue, 16 Jun 2020 08:50:52: start model_add_line... INFO @ Tue, 16 Jun 2020 08:50:52: start X-correlation... INFO @ Tue, 16 Jun 2020 08:50:52: end of X-cor INFO @ Tue, 16 Jun 2020 08:50:52: #2 finished! INFO @ Tue, 16 Jun 2020 08:50:52: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:50:52: #2 alternative fragment length(s) may be 1,67 bps INFO @ Tue, 16 Jun 2020 08:50:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.10_model.r WARNING @ Tue, 16 Jun 2020 08:50:52: #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 08:50:52: #2 You may need to consider one of the other alternative d(s): 1,67 WARNING @ Tue, 16 Jun 2020 08:50:52: #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 08:50:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:50:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:50:55: 13000000 INFO @ Tue, 16 Jun 2020 08:51:03: 14000000 INFO @ Tue, 16 Jun 2020 08:51:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:10: 15000000 INFO @ Tue, 16 Jun 2020 08:51:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.05_summits.bed INFO @ Tue, 16 Jun 2020 08:51:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:51:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:17: 16000000 INFO @ Tue, 16 Jun 2020 08:51:24: 17000000 INFO @ Tue, 16 Jun 2020 08:51:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.10_summits.bed INFO @ Tue, 16 Jun 2020 08:51:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:51:31: 18000000 INFO @ Tue, 16 Jun 2020 08:51:35: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 08:51:35: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 08:51:35: #1 total tags in treatment: 18547901 INFO @ Tue, 16 Jun 2020 08:51:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:35: #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 08:51:36: #1 tags after filtering in treatment: 18547901 INFO @ Tue, 16 Jun 2020 08:51:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:51:36: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:51:37: #2 number of paired peaks: 1017 INFO @ Tue, 16 Jun 2020 08:51:37: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:37: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:37: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:51:37: #2 alternative fragment length(s) may be 1,67 bps INFO @ Tue, 16 Jun 2020 08:51:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.20_model.r WARNING @ Tue, 16 Jun 2020 08:51:37: #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 08:51:37: #2 You may need to consider one of the other alternative d(s): 1,67 WARNING @ Tue, 16 Jun 2020 08:51:37: #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 08:51:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:52:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:52:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:52:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:52:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710287/SRX2710287.20_summits.bed INFO @ Tue, 16 Jun 2020 08:52:15: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling