Job ID = 6368022 SRX = SRX466485 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:23:18 prefetch.2.10.7: 1) Downloading 'SRR1163551'... 2020-06-16T00:23:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:24:52 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:24:52 prefetch.2.10.7: 'SRR1163551' is valid 2020-06-16T00:24:52 prefetch.2.10.7: 1) 'SRR1163551' was downloaded successfully Read 13254411 spots for SRR1163551/SRR1163551.sra Written 13254411 spots for SRR1163551/SRR1163551.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: 00:02:58 13254411 reads; of these: 13254411 (100.00%) were unpaired; of these: 650898 (4.91%) aligned 0 times 11035964 (83.26%) aligned exactly 1 time 1567549 (11.83%) aligned >1 times 95.09% overall alignment rate Time searching: 00:02:58 Overall time: 00:02:58 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] 1764800 / 12603513 = 0.1400 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 09:31:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.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 09:31:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:58: 1000000 INFO @ Tue, 16 Jun 2020 09:32:03: 2000000 INFO @ Tue, 16 Jun 2020 09:32:09: 3000000 INFO @ Tue, 16 Jun 2020 09:32:15: 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 09:32:20: 5000000 INFO @ Tue, 16 Jun 2020 09:32:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.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 09:32:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:26: 6000000 INFO @ Tue, 16 Jun 2020 09:32:27: 1000000 INFO @ Tue, 16 Jun 2020 09:32:32: 7000000 INFO @ Tue, 16 Jun 2020 09:32:32: 2000000 INFO @ Tue, 16 Jun 2020 09:32:37: 3000000 INFO @ Tue, 16 Jun 2020 09:32:38: 8000000 INFO @ Tue, 16 Jun 2020 09:32:42: 4000000 INFO @ Tue, 16 Jun 2020 09:32:44: 9000000 INFO @ Tue, 16 Jun 2020 09:32:47: 5000000 INFO @ Tue, 16 Jun 2020 09:32:50: 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 09:32:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.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 09:32:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:52: 6000000 INFO @ Tue, 16 Jun 2020 09:32:55: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:32:55: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:32:55: #1 total tags in treatment: 10838713 INFO @ Tue, 16 Jun 2020 09:32:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:55: #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 09:32:55: #1 tags after filtering in treatment: 10838713 INFO @ Tue, 16 Jun 2020 09:32:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:32:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:56: #2 number of paired peaks: 199 WARNING @ Tue, 16 Jun 2020 09:32:56: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:56: #2 predicted fragment length is 54 bps INFO @ Tue, 16 Jun 2020 09:32:56: #2 alternative fragment length(s) may be 3,54,548,568,573 bps INFO @ Tue, 16 Jun 2020 09:32:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.05_model.r WARNING @ Tue, 16 Jun 2020 09:32:56: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:32:56: #2 You may need to consider one of the other alternative d(s): 3,54,548,568,573 WARNING @ Tue, 16 Jun 2020 09:32:56: #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 09:32:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:57: 7000000 INFO @ Tue, 16 Jun 2020 09:32:58: 1000000 INFO @ Tue, 16 Jun 2020 09:33:03: 8000000 INFO @ Tue, 16 Jun 2020 09:33:04: 2000000 INFO @ Tue, 16 Jun 2020 09:33:08: 9000000 INFO @ Tue, 16 Jun 2020 09:33:09: 3000000 INFO @ Tue, 16 Jun 2020 09:33:14: 10000000 INFO @ Tue, 16 Jun 2020 09:33:15: 4000000 INFO @ Tue, 16 Jun 2020 09:33:18: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:33:18: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:33:18: #1 total tags in treatment: 10838713 INFO @ Tue, 16 Jun 2020 09:33:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:18: #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 09:33:19: #1 tags after filtering in treatment: 10838713 INFO @ Tue, 16 Jun 2020 09:33:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:19: #2 number of paired peaks: 199 WARNING @ Tue, 16 Jun 2020 09:33:19: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:19: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:19: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:19: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:19: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:19: #2 predicted fragment length is 54 bps INFO @ Tue, 16 Jun 2020 09:33:19: #2 alternative fragment length(s) may be 3,54,548,568,573 bps INFO @ Tue, 16 Jun 2020 09:33:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.10_model.r WARNING @ Tue, 16 Jun 2020 09:33:19: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:33:19: #2 You may need to consider one of the other alternative d(s): 3,54,548,568,573 WARNING @ Tue, 16 Jun 2020 09:33:19: #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 09:33:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:21: 5000000 INFO @ Tue, 16 Jun 2020 09:33:26: 6000000 INFO @ Tue, 16 Jun 2020 09:33:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.05_summits.bed INFO @ Tue, 16 Jun 2020 09:33:31: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1072 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:33:32: 7000000 INFO @ Tue, 16 Jun 2020 09:33:38: 8000000 INFO @ Tue, 16 Jun 2020 09:33:43: 9000000 INFO @ Tue, 16 Jun 2020 09:33:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:49: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:33:54: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:33:54: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:33:54: #1 total tags in treatment: 10838713 INFO @ Tue, 16 Jun 2020 09:33:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:54: #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 09:33:54: #1 tags after filtering in treatment: 10838713 INFO @ Tue, 16 Jun 2020 09:33:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:33:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:55: #2 number of paired peaks: 199 WARNING @ Tue, 16 Jun 2020 09:33:55: Fewer paired peaks (199) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 199 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:55: #2 predicted fragment length is 54 bps INFO @ Tue, 16 Jun 2020 09:33:55: #2 alternative fragment length(s) may be 3,54,548,568,573 bps INFO @ Tue, 16 Jun 2020 09:33:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.20_model.r WARNING @ Tue, 16 Jun 2020 09:33:55: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:33:55: #2 You may need to consider one of the other alternative d(s): 3,54,548,568,573 WARNING @ Tue, 16 Jun 2020 09:33:55: #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 09:33:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.10_summits.bed INFO @ Tue, 16 Jun 2020 09:33:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (337 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:34:17: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:34:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466485/SRX466485.20_summits.bed INFO @ Tue, 16 Jun 2020 09:34:28: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (112 records, 4 fields): 3 millis CompletedMACS2peakCalling