Job ID = 6367896 SRX = SRX4194185 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:45:32 prefetch.2.10.7: 1) Downloading 'SRR7291441'... 2020-06-15T23:45:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:32 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:32 prefetch.2.10.7: 'SRR7291441' is valid 2020-06-15T23:47:32 prefetch.2.10.7: 1) 'SRR7291441' was downloaded successfully 2020-06-15T23:47:32 prefetch.2.10.7: 'SRR7291441' has 0 unresolved dependencies Read 5138414 spots for SRR7291441/SRR7291441.sra Written 5138414 spots for SRR7291441/SRR7291441.sra 2020-06-15T23:48:06 prefetch.2.10.7: 1) Downloading 'SRR7291442'... 2020-06-15T23:48:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:16 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:16 prefetch.2.10.7: 'SRR7291442' is valid 2020-06-15T23:49:16 prefetch.2.10.7: 1) 'SRR7291442' was downloaded successfully 2020-06-15T23:49:16 prefetch.2.10.7: 'SRR7291442' has 0 unresolved dependencies Read 5028817 spots for SRR7291442/SRR7291442.sra Written 5028817 spots for SRR7291442/SRR7291442.sra 2020-06-15T23:49:48 prefetch.2.10.7: 1) Downloading 'SRR7291443'... 2020-06-15T23:49:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:50:48 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:50:48 prefetch.2.10.7: 'SRR7291443' is valid 2020-06-15T23:50:48 prefetch.2.10.7: 1) 'SRR7291443' was downloaded successfully 2020-06-15T23:50:48 prefetch.2.10.7: 'SRR7291443' has 0 unresolved dependencies Read 5110379 spots for SRR7291443/SRR7291443.sra Written 5110379 spots for SRR7291443/SRR7291443.sra 2020-06-15T23:51:20 prefetch.2.10.7: 1) Downloading 'SRR7291444'... 2020-06-15T23:51:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:52:19 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:52:19 prefetch.2.10.7: 'SRR7291444' is valid 2020-06-15T23:52:19 prefetch.2.10.7: 1) 'SRR7291444' was downloaded successfully 2020-06-15T23:52:19 prefetch.2.10.7: 'SRR7291444' has 0 unresolved dependencies Read 4982515 spots for SRR7291444/SRR7291444.sra Written 4982515 spots for SRR7291444/SRR7291444.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: 00:08:42 20260125 reads; of these: 20260125 (100.00%) were unpaired; of these: 390213 (1.93%) aligned 0 times 15389588 (75.96%) aligned exactly 1 time 4480324 (22.11%) aligned >1 times 98.07% overall alignment rate Time searching: 00:08:43 Overall time: 00:08:43 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] 12117460 / 19869912 = 0.6098 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 09:06:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.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 09:06:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:06:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:07:04: 1000000 INFO @ Tue, 16 Jun 2020 09:07:12: 2000000 INFO @ Tue, 16 Jun 2020 09:07:20: 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 09:07:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.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 09:07:26: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:07:26: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:07:28: 4000000 INFO @ Tue, 16 Jun 2020 09:07:34: 1000000 INFO @ Tue, 16 Jun 2020 09:07:37: 5000000 INFO @ Tue, 16 Jun 2020 09:07:42: 2000000 INFO @ Tue, 16 Jun 2020 09:07:46: 6000000 INFO @ Tue, 16 Jun 2020 09:07:51: 3000000 INFO @ Tue, 16 Jun 2020 09:07:54: 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 09:07:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.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 09:07:56: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:07:56: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:07:59: 4000000 INFO @ Tue, 16 Jun 2020 09:08:00: #1 tag size is determined as 55 bps INFO @ Tue, 16 Jun 2020 09:08:00: #1 tag size = 55 INFO @ Tue, 16 Jun 2020 09:08:00: #1 total tags in treatment: 7752452 INFO @ Tue, 16 Jun 2020 09:08:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:08:00: #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 09:08:00: #1 tags after filtering in treatment: 7752452 INFO @ Tue, 16 Jun 2020 09:08:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:08:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:08:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:08:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:08:01: #2 number of paired peaks: 845 WARNING @ Tue, 16 Jun 2020 09:08:01: Fewer paired peaks (845) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 845 pairs to build model! INFO @ Tue, 16 Jun 2020 09:08:01: start model_add_line... INFO @ Tue, 16 Jun 2020 09:08:01: start X-correlation... INFO @ Tue, 16 Jun 2020 09:08:01: end of X-cor INFO @ Tue, 16 Jun 2020 09:08:01: #2 finished! INFO @ Tue, 16 Jun 2020 09:08:01: #2 predicted fragment length is 69 bps INFO @ Tue, 16 Jun 2020 09:08:01: #2 alternative fragment length(s) may be 4,69 bps INFO @ Tue, 16 Jun 2020 09:08:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.05_model.r WARNING @ Tue, 16 Jun 2020 09:08:01: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:08:01: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Tue, 16 Jun 2020 09:08:01: #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 09:08:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:08:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:08:05: 1000000 INFO @ Tue, 16 Jun 2020 09:08:07: 5000000 INFO @ Tue, 16 Jun 2020 09:08:13: 2000000 INFO @ Tue, 16 Jun 2020 09:08:15: 6000000 INFO @ Tue, 16 Jun 2020 09:08:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:08:22: 3000000 INFO @ Tue, 16 Jun 2020 09:08:23: 7000000 INFO @ Tue, 16 Jun 2020 09:08:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:08:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:08:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.05_summits.bed INFO @ Tue, 16 Jun 2020 09:08:26: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1892 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:08:29: #1 tag size is determined as 55 bps INFO @ Tue, 16 Jun 2020 09:08:29: #1 tag size = 55 INFO @ Tue, 16 Jun 2020 09:08:29: #1 total tags in treatment: 7752452 INFO @ Tue, 16 Jun 2020 09:08:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:08:29: #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 09:08:29: #1 tags after filtering in treatment: 7752452 INFO @ Tue, 16 Jun 2020 09:08:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:08:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:08:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:08:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:08:30: #2 number of paired peaks: 845 WARNING @ Tue, 16 Jun 2020 09:08:30: Fewer paired peaks (845) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 845 pairs to build model! INFO @ Tue, 16 Jun 2020 09:08:30: start model_add_line... INFO @ Tue, 16 Jun 2020 09:08:30: start X-correlation... INFO @ Tue, 16 Jun 2020 09:08:30: end of X-cor INFO @ Tue, 16 Jun 2020 09:08:30: #2 finished! INFO @ Tue, 16 Jun 2020 09:08:30: #2 predicted fragment length is 69 bps INFO @ Tue, 16 Jun 2020 09:08:30: #2 alternative fragment length(s) may be 4,69 bps INFO @ Tue, 16 Jun 2020 09:08:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.10_model.r WARNING @ Tue, 16 Jun 2020 09:08:30: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:08:30: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Tue, 16 Jun 2020 09:08:30: #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 09:08:30: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:08:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:08:31: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:08:38: 5000000 INFO @ Tue, 16 Jun 2020 09:08:46: 6000000 INFO @ Tue, 16 Jun 2020 09:08:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:08:53: 7000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:08:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:08:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:08:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.10_summits.bed INFO @ Tue, 16 Jun 2020 09:08:56: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (846 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:08:59: #1 tag size is determined as 55 bps INFO @ Tue, 16 Jun 2020 09:08:59: #1 tag size = 55 INFO @ Tue, 16 Jun 2020 09:08:59: #1 total tags in treatment: 7752452 INFO @ Tue, 16 Jun 2020 09:08:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:08:59: #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 09:08:59: #1 tags after filtering in treatment: 7752452 INFO @ Tue, 16 Jun 2020 09:08:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:08:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:08:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:08:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:00: #2 number of paired peaks: 845 WARNING @ Tue, 16 Jun 2020 09:09:00: Fewer paired peaks (845) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 845 pairs to build model! INFO @ Tue, 16 Jun 2020 09:09:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:00: #2 predicted fragment length is 69 bps INFO @ Tue, 16 Jun 2020 09:09:00: #2 alternative fragment length(s) may be 4,69 bps INFO @ Tue, 16 Jun 2020 09:09:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.20_model.r WARNING @ Tue, 16 Jun 2020 09:09:00: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:09:00: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Tue, 16 Jun 2020 09:09:00: #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 09:09:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:09:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:09:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:09:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:09:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194185/SRX4194185.20_summits.bed INFO @ Tue, 16 Jun 2020 09:09:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (370 records, 4 fields): 1 millis CompletedMACS2peakCalling