Job ID = 6367967 SRX = SRX4456926 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:01:03 prefetch.2.10.7: 1) Downloading 'SRR7591867'... 2020-06-16T00:01:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:01:44 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:01:44 prefetch.2.10.7: 'SRR7591867' is valid 2020-06-16T00:01:44 prefetch.2.10.7: 1) 'SRR7591867' was downloaded successfully Read 7849928 spots for SRR7591867/SRR7591867.sra Written 7849928 spots for SRR7591867/SRR7591867.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: 00:01:34 7849928 reads; of these: 7849928 (100.00%) were unpaired; of these: 1154057 (14.70%) aligned 0 times 5693028 (72.52%) aligned exactly 1 time 1002843 (12.78%) aligned >1 times 85.30% overall alignment rate Time searching: 00:01:34 Overall time: 00:01:34 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] 656372 / 6695871 = 0.0980 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 09:06:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.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 09:06:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:06:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:11: 1000000 INFO @ Tue, 16 Jun 2020 09:06:17: 2000000 INFO @ Tue, 16 Jun 2020 09:06:23: 3000000 INFO @ Tue, 16 Jun 2020 09:06:29: 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 09:06:35: 5000000 INFO @ Tue, 16 Jun 2020 09:06:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.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 09:06:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:06:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:41: 6000000 INFO @ Tue, 16 Jun 2020 09:06:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:06:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:06:41: #1 total tags in treatment: 6039499 INFO @ Tue, 16 Jun 2020 09:06:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:06:41: #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 09:06:42: 1000000 INFO @ Tue, 16 Jun 2020 09:06:42: #1 tags after filtering in treatment: 6039499 INFO @ Tue, 16 Jun 2020 09:06:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:06:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:06:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:06:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:06:42: #2 number of paired peaks: 1004 INFO @ Tue, 16 Jun 2020 09:06:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:06:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:06:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:06:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:06:42: #2 predicted fragment length is 100 bps INFO @ Tue, 16 Jun 2020 09:06:42: #2 alternative fragment length(s) may be 4,100,110 bps INFO @ Tue, 16 Jun 2020 09:06:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.05_model.r WARNING @ Tue, 16 Jun 2020 09:06:42: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:06:42: #2 You may need to consider one of the other alternative d(s): 4,100,110 WARNING @ Tue, 16 Jun 2020 09:06:42: #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 09:06:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:06:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:06:48: 2000000 INFO @ Tue, 16 Jun 2020 09:06:54: 3000000 INFO @ Tue, 16 Jun 2020 09:06:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:07:01: 4000000 INFO @ Tue, 16 Jun 2020 09:07:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:07:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:07:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.05_summits.bed INFO @ Tue, 16 Jun 2020 09:07:03: Done! 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 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1504 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:07:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.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 09:07:05: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:07:05: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:07:07: 5000000 INFO @ Tue, 16 Jun 2020 09:07:11: 1000000 INFO @ Tue, 16 Jun 2020 09:07:13: 6000000 INFO @ Tue, 16 Jun 2020 09:07:14: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:07:14: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:07:14: #1 total tags in treatment: 6039499 INFO @ Tue, 16 Jun 2020 09:07:14: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:07:14: #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 09:07:14: #1 tags after filtering in treatment: 6039499 INFO @ Tue, 16 Jun 2020 09:07:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:07:14: #1 finished! INFO @ Tue, 16 Jun 2020 09:07:14: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:07:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:07:14: #2 number of paired peaks: 1004 INFO @ Tue, 16 Jun 2020 09:07:14: start model_add_line... INFO @ Tue, 16 Jun 2020 09:07:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:07:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:07:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:07:14: #2 predicted fragment length is 100 bps INFO @ Tue, 16 Jun 2020 09:07:14: #2 alternative fragment length(s) may be 4,100,110 bps INFO @ Tue, 16 Jun 2020 09:07:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.10_model.r WARNING @ Tue, 16 Jun 2020 09:07:14: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:07:14: #2 You may need to consider one of the other alternative d(s): 4,100,110 WARNING @ Tue, 16 Jun 2020 09:07:14: #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 09:07:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:07:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:07:17: 2000000 INFO @ Tue, 16 Jun 2020 09:07:22: 3000000 INFO @ Tue, 16 Jun 2020 09:07:28: 4000000 INFO @ Tue, 16 Jun 2020 09:07:28: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:07:33: 5000000 INFO @ Tue, 16 Jun 2020 09:07:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:07:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:07:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.10_summits.bed INFO @ Tue, 16 Jun 2020 09:07:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (623 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:07:39: 6000000 INFO @ Tue, 16 Jun 2020 09:07:39: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:07:39: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:07:39: #1 total tags in treatment: 6039499 INFO @ Tue, 16 Jun 2020 09:07:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:07:39: #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 09:07:39: #1 tags after filtering in treatment: 6039499 INFO @ Tue, 16 Jun 2020 09:07:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:07:39: #1 finished! INFO @ Tue, 16 Jun 2020 09:07:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:07:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:07:40: #2 number of paired peaks: 1004 INFO @ Tue, 16 Jun 2020 09:07:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:07:40: start X-correlation... INFO @ Tue, 16 Jun 2020 09:07:40: end of X-cor INFO @ Tue, 16 Jun 2020 09:07:40: #2 finished! INFO @ Tue, 16 Jun 2020 09:07:40: #2 predicted fragment length is 100 bps INFO @ Tue, 16 Jun 2020 09:07:40: #2 alternative fragment length(s) may be 4,100,110 bps INFO @ Tue, 16 Jun 2020 09:07:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.20_model.r WARNING @ Tue, 16 Jun 2020 09:07:40: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:07:40: #2 You may need to consider one of the other alternative d(s): 4,100,110 WARNING @ Tue, 16 Jun 2020 09:07:40: #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 09:07:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:07:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:07:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:08:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:08:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:08:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4456926/SRX4456926.20_summits.bed INFO @ Tue, 16 Jun 2020 09:08:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (243 records, 4 fields): 1 millis CompletedMACS2peakCalling