Job ID = 6367972 SRX = SRX4456931 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:46:48 prefetch.2.10.7: 1) Downloading 'SRR7591872'... 2020-06-15T23:46:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:55 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:55 prefetch.2.10.7: 'SRR7591872' is valid 2020-06-15T23:47:55 prefetch.2.10.7: 1) 'SRR7591872' was downloaded successfully Read 5330979 spots for SRR7591872/SRR7591872.sra Written 5330979 spots for SRR7591872/SRR7591872.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: 00:01:05 5330979 reads; of these: 5330979 (100.00%) were unpaired; of these: 609875 (11.44%) aligned 0 times 3385408 (63.50%) aligned exactly 1 time 1335696 (25.06%) aligned >1 times 88.56% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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] 453195 / 4721104 = 0.0960 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 08:50:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.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 08:50:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:50:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:51:02: 1000000 INFO @ Tue, 16 Jun 2020 08:51:07: 2000000 INFO @ Tue, 16 Jun 2020 08:51:11: 3000000 INFO @ Tue, 16 Jun 2020 08:51:16: 4000000 INFO @ Tue, 16 Jun 2020 08:51:17: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:51:17: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:51:17: #1 total tags in treatment: 4267909 INFO @ Tue, 16 Jun 2020 08:51:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:17: #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 08:51:17: #1 tags after filtering in treatment: 4267909 INFO @ Tue, 16 Jun 2020 08:51:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:51:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:51:18: #2 number of paired peaks: 1586 INFO @ Tue, 16 Jun 2020 08:51:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:18: #2 predicted fragment length is 60 bps INFO @ Tue, 16 Jun 2020 08:51:18: #2 alternative fragment length(s) may be 3,60 bps INFO @ Tue, 16 Jun 2020 08:51:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.05_model.r WARNING @ Tue, 16 Jun 2020 08:51:18: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:51:18: #2 You may need to consider one of the other alternative d(s): 3,60 WARNING @ Tue, 16 Jun 2020 08:51:18: #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 08:51:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:18: #3 Pre-compute pvalue-qvalue table... 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 08:51:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.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 08:51:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:51:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:51:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:51:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:51:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.05_summits.bed INFO @ Tue, 16 Jun 2020 08:51:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (580 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:51:32: 1000000 INFO @ Tue, 16 Jun 2020 08:51:36: 2000000 INFO @ Tue, 16 Jun 2020 08:51:41: 3000000 INFO @ Tue, 16 Jun 2020 08:51:46: 4000000 INFO @ Tue, 16 Jun 2020 08:51:47: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:51:47: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:51:47: #1 total tags in treatment: 4267909 INFO @ Tue, 16 Jun 2020 08:51:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:51:47: #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 08:51:47: #1 tags after filtering in treatment: 4267909 INFO @ Tue, 16 Jun 2020 08:51:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:51:47: #1 finished! INFO @ Tue, 16 Jun 2020 08:51:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:51:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:51:47: #2 number of paired peaks: 1586 INFO @ Tue, 16 Jun 2020 08:51:47: start model_add_line... INFO @ Tue, 16 Jun 2020 08:51:47: start X-correlation... INFO @ Tue, 16 Jun 2020 08:51:47: end of X-cor INFO @ Tue, 16 Jun 2020 08:51:47: #2 finished! INFO @ Tue, 16 Jun 2020 08:51:47: #2 predicted fragment length is 60 bps INFO @ Tue, 16 Jun 2020 08:51:47: #2 alternative fragment length(s) may be 3,60 bps INFO @ Tue, 16 Jun 2020 08:51:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.10_model.r WARNING @ Tue, 16 Jun 2020 08:51:47: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:51:47: #2 You may need to consider one of the other alternative d(s): 3,60 WARNING @ Tue, 16 Jun 2020 08:51:47: #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 08:51:47: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:51:47: #3 Pre-compute pvalue-qvalue table... 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 08:51:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:51:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.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 08:51:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:51:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:52:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:52:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:52:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.10_summits.bed INFO @ Tue, 16 Jun 2020 08:52:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (355 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:52:02: 1000000 INFO @ Tue, 16 Jun 2020 08:52:06: 2000000 INFO @ Tue, 16 Jun 2020 08:52:11: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:52:16: 4000000 INFO @ Tue, 16 Jun 2020 08:52:17: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:52:17: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:52:17: #1 total tags in treatment: 4267909 INFO @ Tue, 16 Jun 2020 08:52:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:52:17: #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 08:52:17: #1 tags after filtering in treatment: 4267909 INFO @ Tue, 16 Jun 2020 08:52:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:52:17: #1 finished! INFO @ Tue, 16 Jun 2020 08:52:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:52:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:52:18: #2 number of paired peaks: 1586 INFO @ Tue, 16 Jun 2020 08:52:18: start model_add_line... INFO @ Tue, 16 Jun 2020 08:52:18: start X-correlation... INFO @ Tue, 16 Jun 2020 08:52:18: end of X-cor INFO @ Tue, 16 Jun 2020 08:52:18: #2 finished! INFO @ Tue, 16 Jun 2020 08:52:18: #2 predicted fragment length is 60 bps INFO @ Tue, 16 Jun 2020 08:52:18: #2 alternative fragment length(s) may be 3,60 bps INFO @ Tue, 16 Jun 2020 08:52:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.20_model.r WARNING @ Tue, 16 Jun 2020 08:52:18: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:52:18: #2 You may need to consider one of the other alternative d(s): 3,60 WARNING @ Tue, 16 Jun 2020 08:52:18: #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 08:52:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:52:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:52:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:52:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:52:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:52:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456931/SRX4456931.20_summits.bed INFO @ Tue, 16 Jun 2020 08:52:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (167 records, 4 fields): 1 millis CompletedMACS2peakCalling