Job ID = 6366836 SRX = SRX2350735 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:05:38 prefetch.2.10.7: 1) Downloading 'SRR5024044'... 2020-06-15T23:05:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:07:02 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:07:02 prefetch.2.10.7: 1) 'SRR5024044' was downloaded successfully Read 15570342 spots for SRR5024044/SRR5024044.sra Written 15570342 spots for SRR5024044/SRR5024044.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:52 15570342 reads; of these: 15570342 (100.00%) were unpaired; of these: 297871 (1.91%) aligned 0 times 12070165 (77.52%) aligned exactly 1 time 3202306 (20.57%) aligned >1 times 98.09% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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] 2208051 / 15272471 = 0.1446 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 08:15:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.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 08:15:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:42: 1000000 INFO @ Tue, 16 Jun 2020 08:15:48: 2000000 INFO @ Tue, 16 Jun 2020 08:15:54: 3000000 INFO @ Tue, 16 Jun 2020 08:15:59: 4000000 INFO @ Tue, 16 Jun 2020 08:16:04: 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 08:16:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.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 08:16:07: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:16:07: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:16:10: 6000000 INFO @ Tue, 16 Jun 2020 08:16:13: 1000000 INFO @ Tue, 16 Jun 2020 08:16:16: 7000000 INFO @ Tue, 16 Jun 2020 08:16:19: 2000000 INFO @ Tue, 16 Jun 2020 08:16:22: 8000000 INFO @ Tue, 16 Jun 2020 08:16:24: 3000000 INFO @ Tue, 16 Jun 2020 08:16:28: 9000000 INFO @ Tue, 16 Jun 2020 08:16:30: 4000000 INFO @ Tue, 16 Jun 2020 08:16:33: 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 08:16:36: 5000000 INFO @ Tue, 16 Jun 2020 08:16:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.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 08:16:37: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:16:37: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:16:39: 11000000 INFO @ Tue, 16 Jun 2020 08:16:42: 6000000 INFO @ Tue, 16 Jun 2020 08:16:43: 1000000 INFO @ Tue, 16 Jun 2020 08:16:45: 12000000 INFO @ Tue, 16 Jun 2020 08:16:48: 7000000 INFO @ Tue, 16 Jun 2020 08:16:49: 2000000 INFO @ Tue, 16 Jun 2020 08:16:51: 13000000 INFO @ Tue, 16 Jun 2020 08:16:51: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:16:51: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:16:51: #1 total tags in treatment: 13064420 INFO @ Tue, 16 Jun 2020 08:16:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:51: #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 08:16:52: #1 tags after filtering in treatment: 13064420 INFO @ Tue, 16 Jun 2020 08:16:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:52: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:52: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:52: #2 number of paired peaks: 361 WARNING @ Tue, 16 Jun 2020 08:16:52: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:52: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:53: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:53: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:16:53: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 08:16:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.05_model.r WARNING @ Tue, 16 Jun 2020 08:16:53: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:16:53: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 08:16:53: #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 08:16:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:16:53: 8000000 INFO @ Tue, 16 Jun 2020 08:16:55: 3000000 INFO @ Tue, 16 Jun 2020 08:16:59: 9000000 INFO @ Tue, 16 Jun 2020 08:17:00: 4000000 INFO @ Tue, 16 Jun 2020 08:17:05: 10000000 INFO @ Tue, 16 Jun 2020 08:17:06: 5000000 INFO @ Tue, 16 Jun 2020 08:17:11: 11000000 INFO @ Tue, 16 Jun 2020 08:17:12: 6000000 INFO @ Tue, 16 Jun 2020 08:17:17: 12000000 INFO @ Tue, 16 Jun 2020 08:17:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:17:18: 7000000 INFO @ Tue, 16 Jun 2020 08:17:22: 13000000 INFO @ Tue, 16 Jun 2020 08:17:23: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:17:23: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:17:23: #1 total tags in treatment: 13064420 INFO @ Tue, 16 Jun 2020 08:17:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:17:23: #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 08:17:23: #1 tags after filtering in treatment: 13064420 INFO @ Tue, 16 Jun 2020 08:17:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:17:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:17:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:17:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:17:24: 8000000 INFO @ Tue, 16 Jun 2020 08:17:24: #2 number of paired peaks: 361 WARNING @ Tue, 16 Jun 2020 08:17:24: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Tue, 16 Jun 2020 08:17:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:17:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:17:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:17:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:17:24: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:17:24: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 08:17:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.10_model.r WARNING @ Tue, 16 Jun 2020 08:17:24: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:17:24: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 08:17:24: #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 08:17:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:17:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:17:29: 9000000 INFO @ Tue, 16 Jun 2020 08:17:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:17:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:17:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.05_summits.bed INFO @ Tue, 16 Jun 2020 08:17:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (786 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:17:35: 10000000 INFO @ Tue, 16 Jun 2020 08:17:40: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:17:46: 12000000 INFO @ Tue, 16 Jun 2020 08:17:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:17:51: 13000000 INFO @ Tue, 16 Jun 2020 08:17:51: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:17:51: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:17:51: #1 total tags in treatment: 13064420 INFO @ Tue, 16 Jun 2020 08:17:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:17:51: #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 08:17:51: #1 tags after filtering in treatment: 13064420 INFO @ Tue, 16 Jun 2020 08:17:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:17:51: #1 finished! INFO @ Tue, 16 Jun 2020 08:17:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:17:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:17:52: #2 number of paired peaks: 361 WARNING @ Tue, 16 Jun 2020 08:17:52: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Tue, 16 Jun 2020 08:17:52: start model_add_line... INFO @ Tue, 16 Jun 2020 08:17:52: start X-correlation... INFO @ Tue, 16 Jun 2020 08:17:53: end of X-cor INFO @ Tue, 16 Jun 2020 08:17:53: #2 finished! INFO @ Tue, 16 Jun 2020 08:17:53: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 08:17:53: #2 alternative fragment length(s) may be 2,47 bps INFO @ Tue, 16 Jun 2020 08:17:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.20_model.r WARNING @ Tue, 16 Jun 2020 08:17:53: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:17:53: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Tue, 16 Jun 2020 08:17:53: #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 08:17:53: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:17:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.10_summits.bed INFO @ Tue, 16 Jun 2020 08:18:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (477 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:18:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:18:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2350735/SRX2350735.20_summits.bed INFO @ Tue, 16 Jun 2020 08:18:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (207 records, 4 fields): 1 millis CompletedMACS2peakCalling