Job ID = 6368620 SRX = SRX5020844 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:21:36 prefetch.2.10.7: 1) Downloading 'SRR8201467'... 2020-06-16T00:21:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:23:21 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:23:22 prefetch.2.10.7: 'SRR8201467' is valid 2020-06-16T00:23:22 prefetch.2.10.7: 1) 'SRR8201467' was downloaded successfully Read 12804073 spots for SRR8201467/SRR8201467.sra Written 12804073 spots for SRR8201467/SRR8201467.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: 00:02:56 12804073 reads; of these: 12804073 (100.00%) were unpaired; of these: 167109 (1.31%) aligned 0 times 10759173 (84.03%) aligned exactly 1 time 1877791 (14.67%) aligned >1 times 98.69% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 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] 2155314 / 12636964 = 0.1706 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 09:31:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.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 09:31:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:35: 1000000 INFO @ Tue, 16 Jun 2020 09:31:40: 2000000 INFO @ Tue, 16 Jun 2020 09:31:46: 3000000 INFO @ Tue, 16 Jun 2020 09:31:51: 4000000 INFO @ Tue, 16 Jun 2020 09:31:56: 5000000 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 09:31:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.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 09:31:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:02: 6000000 INFO @ Tue, 16 Jun 2020 09:32:05: 1000000 INFO @ Tue, 16 Jun 2020 09:32:08: 7000000 INFO @ Tue, 16 Jun 2020 09:32:11: 2000000 INFO @ Tue, 16 Jun 2020 09:32:14: 8000000 INFO @ Tue, 16 Jun 2020 09:32:16: 3000000 INFO @ Tue, 16 Jun 2020 09:32:19: 9000000 INFO @ Tue, 16 Jun 2020 09:32:22: 4000000 INFO @ Tue, 16 Jun 2020 09:32:25: 10000000 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 09:32:28: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:32:28: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:32:28: #1 total tags in treatment: 10481650 INFO @ Tue, 16 Jun 2020 09:32:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:28: #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 09:32:28: 5000000 INFO @ Tue, 16 Jun 2020 09:32:28: #1 tags after filtering in treatment: 10481650 INFO @ Tue, 16 Jun 2020 09:32:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:28: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:29: #2 number of paired peaks: 238 WARNING @ Tue, 16 Jun 2020 09:32:29: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:29: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 09:32:29: #2 alternative fragment length(s) may be 3,53,492,497 bps INFO @ Tue, 16 Jun 2020 09:32:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.05_model.r WARNING @ Tue, 16 Jun 2020 09:32:29: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:32:29: #2 You may need to consider one of the other alternative d(s): 3,53,492,497 WARNING @ Tue, 16 Jun 2020 09:32:29: #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 09:32:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.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 09:32:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:33: 6000000 INFO @ Tue, 16 Jun 2020 09:32:35: 1000000 INFO @ Tue, 16 Jun 2020 09:32:39: 7000000 INFO @ Tue, 16 Jun 2020 09:32:41: 2000000 INFO @ Tue, 16 Jun 2020 09:32:44: 8000000 INFO @ Tue, 16 Jun 2020 09:32:46: 3000000 INFO @ Tue, 16 Jun 2020 09:32:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:32:50: 9000000 INFO @ Tue, 16 Jun 2020 09:32:52: 4000000 INFO @ Tue, 16 Jun 2020 09:32:55: 10000000 INFO @ Tue, 16 Jun 2020 09:32:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:32:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:32:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.05_summits.bed INFO @ Tue, 16 Jun 2020 09:32:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (494 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:32:57: 5000000 INFO @ Tue, 16 Jun 2020 09:32:58: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:32:58: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:32:58: #1 total tags in treatment: 10481650 INFO @ Tue, 16 Jun 2020 09:32:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:58: #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 09:32:58: #1 tags after filtering in treatment: 10481650 INFO @ Tue, 16 Jun 2020 09:32:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:58: #2 number of paired peaks: 238 WARNING @ Tue, 16 Jun 2020 09:32:58: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:59: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 09:32:59: #2 alternative fragment length(s) may be 3,53,492,497 bps INFO @ Tue, 16 Jun 2020 09:32:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.10_model.r WARNING @ Tue, 16 Jun 2020 09:32:59: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:32:59: #2 You may need to consider one of the other alternative d(s): 3,53,492,497 WARNING @ Tue, 16 Jun 2020 09:32:59: #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 09:32:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:02: 6000000 INFO @ Tue, 16 Jun 2020 09:33:08: 7000000 INFO @ Tue, 16 Jun 2020 09:33:13: 8000000 INFO @ Tue, 16 Jun 2020 09:33:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:19: 9000000 INFO @ Tue, 16 Jun 2020 09:33:24: 10000000 INFO @ Tue, 16 Jun 2020 09:33:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.10_summits.bed INFO @ Tue, 16 Jun 2020 09:33:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (292 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:33:26: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:33:26: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:33:26: #1 total tags in treatment: 10481650 INFO @ Tue, 16 Jun 2020 09:33:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:26: #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 09:33:27: #1 tags after filtering in treatment: 10481650 INFO @ Tue, 16 Jun 2020 09:33:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:27: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:27: #2 number of paired peaks: 238 WARNING @ Tue, 16 Jun 2020 09:33:27: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:27: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:28: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:28: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:28: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:28: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 09:33:28: #2 alternative fragment length(s) may be 3,53,492,497 bps INFO @ Tue, 16 Jun 2020 09:33:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.20_model.r WARNING @ Tue, 16 Jun 2020 09:33:28: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:33:28: #2 You may need to consider one of the other alternative d(s): 3,53,492,497 WARNING @ Tue, 16 Jun 2020 09:33:28: #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 09:33:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:28: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:33:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020844/SRX5020844.20_summits.bed INFO @ Tue, 16 Jun 2020 09:33:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (94 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。