Job ID = 6368726 SRX = SRX5402750 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:30:16 prefetch.2.10.7: 1) Downloading 'SRR8602984'... 2020-06-16T00:30:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:36:05 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:36:05 prefetch.2.10.7: 1) 'SRR8602984' was downloaded successfully Read 45111121 spots for SRR8602984/SRR8602984.sra Written 45111121 spots for SRR8602984/SRR8602984.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: 00:06:35 45111121 reads; of these: 45111121 (100.00%) were unpaired; of these: 30420906 (67.44%) aligned 0 times 8150337 (18.07%) aligned exactly 1 time 6539878 (14.50%) aligned >1 times 32.56% overall alignment rate Time searching: 00:06:35 Overall time: 00:06:35 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 8 files... [bam_rmdupse_core] 8402634 / 14690215 = 0.5720 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 09:48:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.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 09:48:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:17: 1000000 INFO @ Tue, 16 Jun 2020 09:48:24: 2000000 INFO @ Tue, 16 Jun 2020 09:48:32: 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 09:48:39: 4000000 INFO @ Tue, 16 Jun 2020 09:48:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.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 09:48:40: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:40: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:47: 5000000 INFO @ Tue, 16 Jun 2020 09:48:47: 1000000 INFO @ Tue, 16 Jun 2020 09:48:55: 2000000 INFO @ Tue, 16 Jun 2020 09:48:55: 6000000 INFO @ Tue, 16 Jun 2020 09:48:58: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:48:58: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:48:58: #1 total tags in treatment: 6287581 INFO @ Tue, 16 Jun 2020 09:48:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:58: #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 09:48:58: #1 tags after filtering in treatment: 6287581 INFO @ Tue, 16 Jun 2020 09:48:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:48:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:48:58: #2 number of paired peaks: 3554 INFO @ Tue, 16 Jun 2020 09:48:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:48:58: start X-correlation... INFO @ Tue, 16 Jun 2020 09:48:58: end of X-cor INFO @ Tue, 16 Jun 2020 09:48:58: #2 finished! INFO @ Tue, 16 Jun 2020 09:48:58: #2 predicted fragment length is 84 bps INFO @ Tue, 16 Jun 2020 09:48:58: #2 alternative fragment length(s) may be 4,84 bps INFO @ Tue, 16 Jun 2020 09:48:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.05_model.r WARNING @ Tue, 16 Jun 2020 09:48:59: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:48:59: #2 You may need to consider one of the other alternative d(s): 4,84 WARNING @ Tue, 16 Jun 2020 09:48:59: #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 09:48:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:48:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:02: 3000000 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 09:49:08: 4000000 INFO @ Tue, 16 Jun 2020 09:49:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.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 09:49:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:16: 5000000 INFO @ Tue, 16 Jun 2020 09:49:17: 1000000 INFO @ Tue, 16 Jun 2020 09:49:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.05_summits.bed INFO @ Tue, 16 Jun 2020 09:49:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5866 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:49:23: 6000000 INFO @ Tue, 16 Jun 2020 09:49:25: 2000000 INFO @ Tue, 16 Jun 2020 09:49:25: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:49:25: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:49:25: #1 total tags in treatment: 6287581 INFO @ Tue, 16 Jun 2020 09:49:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:25: #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 09:49:25: #1 tags after filtering in treatment: 6287581 INFO @ Tue, 16 Jun 2020 09:49:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:26: #2 number of paired peaks: 3554 INFO @ Tue, 16 Jun 2020 09:49:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:26: #2 predicted fragment length is 84 bps INFO @ Tue, 16 Jun 2020 09:49:26: #2 alternative fragment length(s) may be 4,84 bps INFO @ Tue, 16 Jun 2020 09:49:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.10_model.r WARNING @ Tue, 16 Jun 2020 09:49:26: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:49:26: #2 You may need to consider one of the other alternative d(s): 4,84 WARNING @ Tue, 16 Jun 2020 09:49:26: #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 09:49:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:32: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:49:39: 4000000 INFO @ Tue, 16 Jun 2020 09:49:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:46: 5000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:49:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.10_summits.bed INFO @ Tue, 16 Jun 2020 09:49:51: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3170 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:49:53: 6000000 INFO @ Tue, 16 Jun 2020 09:49:55: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:49:55: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:49:55: #1 total tags in treatment: 6287581 INFO @ Tue, 16 Jun 2020 09:49:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:55: #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 09:49:55: #1 tags after filtering in treatment: 6287581 INFO @ Tue, 16 Jun 2020 09:49:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:56: #2 number of paired peaks: 3554 INFO @ Tue, 16 Jun 2020 09:49:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:56: #2 predicted fragment length is 84 bps INFO @ Tue, 16 Jun 2020 09:49:56: #2 alternative fragment length(s) may be 4,84 bps INFO @ Tue, 16 Jun 2020 09:49:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.20_model.r WARNING @ Tue, 16 Jun 2020 09:49:56: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:49:56: #2 You may need to consider one of the other alternative d(s): 4,84 WARNING @ Tue, 16 Jun 2020 09:49:56: #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 09:49:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:50:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402750/SRX5402750.20_summits.bed INFO @ Tue, 16 Jun 2020 09:50:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1261 records, 4 fields): 2 millis CompletedMACS2peakCalling