Job ID = 6529112 SRX = SRX5402769 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:07:11 27498817 reads; of these: 27498817 (100.00%) were unpaired; of these: 1201729 (4.37%) aligned 0 times 21845826 (79.44%) aligned exactly 1 time 4451262 (16.19%) aligned >1 times 95.63% overall alignment rate Time searching: 00:07:11 Overall time: 00:07:11 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 12 files... [bam_rmdupse_core] 9413257 / 26297088 = 0.3580 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, 30 Jun 2020 01:13:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.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, 30 Jun 2020 01:13:53: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:13:53: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:13:59: 1000000 INFO @ Tue, 30 Jun 2020 01:14:05: 2000000 INFO @ Tue, 30 Jun 2020 01:14:11: 3000000 INFO @ Tue, 30 Jun 2020 01:14:18: 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, 30 Jun 2020 01:14:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.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, 30 Jun 2020 01:14:23: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:14:23: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:14:24: 5000000 INFO @ Tue, 30 Jun 2020 01:14:30: 6000000 INFO @ Tue, 30 Jun 2020 01:14:31: 1000000 INFO @ Tue, 30 Jun 2020 01:14:37: 7000000 INFO @ Tue, 30 Jun 2020 01:14:38: 2000000 INFO @ Tue, 30 Jun 2020 01:14:43: 8000000 INFO @ Tue, 30 Jun 2020 01:14:46: 3000000 INFO @ Tue, 30 Jun 2020 01:14:49: 9000000 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, 30 Jun 2020 01:14:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.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, 30 Jun 2020 01:14:53: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:14:53: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:14:54: 4000000 INFO @ Tue, 30 Jun 2020 01:14:56: 10000000 INFO @ Tue, 30 Jun 2020 01:15:01: 1000000 INFO @ Tue, 30 Jun 2020 01:15:02: 5000000 INFO @ Tue, 30 Jun 2020 01:15:04: 11000000 INFO @ Tue, 30 Jun 2020 01:15:08: 2000000 INFO @ Tue, 30 Jun 2020 01:15:10: 6000000 INFO @ Tue, 30 Jun 2020 01:15:11: 12000000 INFO @ Tue, 30 Jun 2020 01:15:15: 3000000 INFO @ Tue, 30 Jun 2020 01:15:18: 7000000 INFO @ Tue, 30 Jun 2020 01:15:19: 13000000 INFO @ Tue, 30 Jun 2020 01:15:23: 4000000 INFO @ Tue, 30 Jun 2020 01:15:26: 14000000 INFO @ Tue, 30 Jun 2020 01:15:27: 8000000 INFO @ Tue, 30 Jun 2020 01:15:30: 5000000 INFO @ Tue, 30 Jun 2020 01:15:33: 15000000 INFO @ Tue, 30 Jun 2020 01:15:35: 9000000 INFO @ Tue, 30 Jun 2020 01:15:37: 6000000 INFO @ Tue, 30 Jun 2020 01:15:41: 16000000 INFO @ Tue, 30 Jun 2020 01:15:43: 10000000 INFO @ Tue, 30 Jun 2020 01:15:45: 7000000 INFO @ Tue, 30 Jun 2020 01:15:47: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:15:47: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:15:47: #1 total tags in treatment: 16883831 INFO @ Tue, 30 Jun 2020 01:15:47: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:15:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:15:47: #1 tags after filtering in treatment: 16883831 INFO @ Tue, 30 Jun 2020 01:15:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:15:47: #1 finished! INFO @ Tue, 30 Jun 2020 01:15:47: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:15:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:15:49: #2 number of paired peaks: 326 WARNING @ Tue, 30 Jun 2020 01:15:49: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Tue, 30 Jun 2020 01:15:49: start model_add_line... INFO @ Tue, 30 Jun 2020 01:15:49: start X-correlation... INFO @ Tue, 30 Jun 2020 01:15:49: end of X-cor INFO @ Tue, 30 Jun 2020 01:15:49: #2 finished! INFO @ Tue, 30 Jun 2020 01:15:49: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 01:15:49: #2 alternative fragment length(s) may be 1,46,559,577 bps INFO @ Tue, 30 Jun 2020 01:15:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.05_model.r WARNING @ Tue, 30 Jun 2020 01:15:49: #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, 30 Jun 2020 01:15:49: #2 You may need to consider one of the other alternative d(s): 1,46,559,577 WARNING @ Tue, 30 Jun 2020 01:15:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:15:49: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:15:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:15:51: 11000000 INFO @ Tue, 30 Jun 2020 01:15:52: 8000000 INFO @ Tue, 30 Jun 2020 01:15:58: 9000000 INFO @ Tue, 30 Jun 2020 01:16:00: 12000000 INFO @ Tue, 30 Jun 2020 01:16:05: 10000000 INFO @ Tue, 30 Jun 2020 01:16:08: 13000000 INFO @ Tue, 30 Jun 2020 01:16:12: 11000000 INFO @ Tue, 30 Jun 2020 01:16:16: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:16:16: 14000000 INFO @ Tue, 30 Jun 2020 01:16:18: 12000000 INFO @ Tue, 30 Jun 2020 01:16:24: 15000000 INFO @ Tue, 30 Jun 2020 01:16:25: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:16:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:16:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:16:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.05_summits.bed INFO @ Tue, 30 Jun 2020 01:16:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (774 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:16:31: 14000000 INFO @ Tue, 30 Jun 2020 01:16:32: 16000000 INFO @ Tue, 30 Jun 2020 01:16:38: 15000000 INFO @ Tue, 30 Jun 2020 01:16:39: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:16:39: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:16:39: #1 total tags in treatment: 16883831 INFO @ Tue, 30 Jun 2020 01:16:39: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:16:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:16:40: #1 tags after filtering in treatment: 16883831 INFO @ Tue, 30 Jun 2020 01:16:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:16:40: #1 finished! INFO @ Tue, 30 Jun 2020 01:16:40: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:16:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:16:41: #2 number of paired peaks: 326 WARNING @ Tue, 30 Jun 2020 01:16:41: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Tue, 30 Jun 2020 01:16:41: start model_add_line... INFO @ Tue, 30 Jun 2020 01:16:41: start X-correlation... INFO @ Tue, 30 Jun 2020 01:16:41: end of X-cor INFO @ Tue, 30 Jun 2020 01:16:41: #2 finished! INFO @ Tue, 30 Jun 2020 01:16:41: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 01:16:41: #2 alternative fragment length(s) may be 1,46,559,577 bps INFO @ Tue, 30 Jun 2020 01:16:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.10_model.r WARNING @ Tue, 30 Jun 2020 01:16:41: #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, 30 Jun 2020 01:16:41: #2 You may need to consider one of the other alternative d(s): 1,46,559,577 WARNING @ Tue, 30 Jun 2020 01:16:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:16:41: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:16:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:16:44: 16000000 INFO @ Tue, 30 Jun 2020 01:16:50: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:16:50: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:16:50: #1 total tags in treatment: 16883831 INFO @ Tue, 30 Jun 2020 01:16:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:16:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 01:16:50: #1 tags after filtering in treatment: 16883831 INFO @ Tue, 30 Jun 2020 01:16:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:16:50: #1 finished! INFO @ Tue, 30 Jun 2020 01:16:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:16:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:16:51: #2 number of paired peaks: 326 WARNING @ Tue, 30 Jun 2020 01:16:51: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Tue, 30 Jun 2020 01:16:51: start model_add_line... INFO @ Tue, 30 Jun 2020 01:16:51: start X-correlation... INFO @ Tue, 30 Jun 2020 01:16:51: end of X-cor INFO @ Tue, 30 Jun 2020 01:16:51: #2 finished! INFO @ Tue, 30 Jun 2020 01:16:51: #2 predicted fragment length is 46 bps INFO @ Tue, 30 Jun 2020 01:16:51: #2 alternative fragment length(s) may be 1,46,559,577 bps INFO @ Tue, 30 Jun 2020 01:16:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.20_model.r WARNING @ Tue, 30 Jun 2020 01:16:51: #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, 30 Jun 2020 01:16:51: #2 You may need to consider one of the other alternative d(s): 1,46,559,577 WARNING @ Tue, 30 Jun 2020 01:16:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 01:16:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:16:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:17:08: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:17:18: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:17:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:17:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:17:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.10_summits.bed INFO @ Tue, 30 Jun 2020 01:17:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (487 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:17:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:17:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:17:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402769/SRX5402769.20_summits.bed INFO @ Tue, 30 Jun 2020 01:17:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (199 records, 4 fields): 1 millis CompletedMACS2peakCalling