Job ID = 6368019 SRX = SRX466482 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:06:16 prefetch.2.10.7: 1) Downloading 'SRR1163548'... 2020-06-16T00:06:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:07:45 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:07:45 prefetch.2.10.7: 'SRR1163548' is valid 2020-06-16T00:07:45 prefetch.2.10.7: 1) 'SRR1163548' was downloaded successfully Read 13823502 spots for SRR1163548/SRR1163548.sra Written 13823502 spots for SRR1163548/SRR1163548.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: 00:03:13 13823502 reads; of these: 13823502 (100.00%) were unpaired; of these: 855565 (6.19%) aligned 0 times 9883601 (71.50%) aligned exactly 1 time 3084336 (22.31%) aligned >1 times 93.81% overall alignment rate Time searching: 00:03:13 Overall time: 00:03:13 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] 3856064 / 12967937 = 0.2974 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 09:15:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.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 09:15:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:15:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:15:18: 1000000 INFO @ Tue, 16 Jun 2020 09:15:23: 2000000 INFO @ Tue, 16 Jun 2020 09:15:29: 3000000 INFO @ Tue, 16 Jun 2020 09:15:35: 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 09:15:41: 5000000 INFO @ Tue, 16 Jun 2020 09:15:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.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 09:15:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:15:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:15:47: 6000000 INFO @ Tue, 16 Jun 2020 09:15:50: 1000000 INFO @ Tue, 16 Jun 2020 09:15:54: 7000000 INFO @ Tue, 16 Jun 2020 09:15:57: 2000000 INFO @ Tue, 16 Jun 2020 09:16:00: 8000000 INFO @ Tue, 16 Jun 2020 09:16:03: 3000000 INFO @ Tue, 16 Jun 2020 09:16:07: 9000000 INFO @ Tue, 16 Jun 2020 09:16:07: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:16:07: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:16:07: #1 total tags in treatment: 9111873 INFO @ Tue, 16 Jun 2020 09:16:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:07: #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 09:16:08: #1 tags after filtering in treatment: 9111873 INFO @ Tue, 16 Jun 2020 09:16:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:16:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:08: #2 number of paired peaks: 553 WARNING @ Tue, 16 Jun 2020 09:16:08: Fewer paired peaks (553) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 553 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:08: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 09:16:08: #2 alternative fragment length(s) may be 2,46,528,583 bps INFO @ Tue, 16 Jun 2020 09:16:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.05_model.r WARNING @ Tue, 16 Jun 2020 09:16:08: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:16:08: #2 You may need to consider one of the other alternative d(s): 2,46,528,583 WARNING @ Tue, 16 Jun 2020 09:16:08: #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 09:16:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:10: 4000000 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 09:16:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.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 09:16:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:16:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:16:16: 5000000 INFO @ Tue, 16 Jun 2020 09:16:19: 1000000 INFO @ Tue, 16 Jun 2020 09:16:22: 6000000 INFO @ Tue, 16 Jun 2020 09:16:25: 2000000 INFO @ Tue, 16 Jun 2020 09:16:29: 7000000 INFO @ Tue, 16 Jun 2020 09:16:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:31: 3000000 INFO @ Tue, 16 Jun 2020 09:16:35: 8000000 INFO @ Tue, 16 Jun 2020 09:16:38: 4000000 INFO @ Tue, 16 Jun 2020 09:16:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.05_summits.bed INFO @ Tue, 16 Jun 2020 09:16:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (729 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:16:42: 9000000 INFO @ Tue, 16 Jun 2020 09:16:42: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:16:42: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:16:42: #1 total tags in treatment: 9111873 INFO @ Tue, 16 Jun 2020 09:16:42: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:42: #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 09:16:42: #1 tags after filtering in treatment: 9111873 INFO @ Tue, 16 Jun 2020 09:16:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:16:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:43: #2 number of paired peaks: 553 WARNING @ Tue, 16 Jun 2020 09:16:43: Fewer paired peaks (553) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 553 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:43: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 09:16:43: #2 alternative fragment length(s) may be 2,46,528,583 bps INFO @ Tue, 16 Jun 2020 09:16:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.10_model.r WARNING @ Tue, 16 Jun 2020 09:16:43: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:16:43: #2 You may need to consider one of the other alternative d(s): 2,46,528,583 WARNING @ Tue, 16 Jun 2020 09:16:43: #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 09:16:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:44: 5000000 INFO @ Tue, 16 Jun 2020 09:16:51: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:16:57: 7000000 INFO @ Tue, 16 Jun 2020 09:17:03: 8000000 INFO @ Tue, 16 Jun 2020 09:17:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:09: 9000000 INFO @ Tue, 16 Jun 2020 09:17:10: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:17:10: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:17:10: #1 total tags in treatment: 9111873 INFO @ Tue, 16 Jun 2020 09:17:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:10: #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 09:17:10: #1 tags after filtering in treatment: 9111873 INFO @ Tue, 16 Jun 2020 09:17:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:17:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:11: #2 number of paired peaks: 553 WARNING @ Tue, 16 Jun 2020 09:17:11: Fewer paired peaks (553) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 553 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:11: #2 predicted fragment length is 46 bps INFO @ Tue, 16 Jun 2020 09:17:11: #2 alternative fragment length(s) may be 2,46,528,583 bps INFO @ Tue, 16 Jun 2020 09:17:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.20_model.r WARNING @ Tue, 16 Jun 2020 09:17:11: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:17:11: #2 You may need to consider one of the other alternative d(s): 2,46,528,583 WARNING @ Tue, 16 Jun 2020 09:17:11: #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 09:17:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:17:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.10_summits.bed INFO @ Tue, 16 Jun 2020 09:17:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (482 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:17:32: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466482/SRX466482.20_summits.bed INFO @ Tue, 16 Jun 2020 09:17:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (195 records, 4 fields): 1 millis CompletedMACS2peakCalling