Job ID = 6366324 SRX = SRX1132920 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:47:37 prefetch.2.10.7: 1) Downloading 'SRR2144369'... 2020-06-15T22:47:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:49:07 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:49:08 prefetch.2.10.7: 'SRR2144369' is valid 2020-06-15T22:49:08 prefetch.2.10.7: 1) 'SRR2144369' was downloaded successfully Read 18240658 spots for SRR2144369/SRR2144369.sra Written 18240658 spots for SRR2144369/SRR2144369.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: 00:00:01 Multiseed full-index search: 00:05:23 18240658 reads; of these: 18240658 (100.00%) were unpaired; of these: 891461 (4.89%) aligned 0 times 14206065 (77.88%) aligned exactly 1 time 3143132 (17.23%) aligned >1 times 95.11% overall alignment rate Time searching: 00:05:24 Overall time: 00:05:24 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] 5759316 / 17349197 = 0.3320 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 08:00:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.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 08:00:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:00:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:03: 1000000 INFO @ Tue, 16 Jun 2020 08:01:10: 2000000 INFO @ Tue, 16 Jun 2020 08:01:18: 3000000 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 08:01:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.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 08:01:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:25: 4000000 INFO @ Tue, 16 Jun 2020 08:01:33: 1000000 INFO @ Tue, 16 Jun 2020 08:01:34: 5000000 INFO @ Tue, 16 Jun 2020 08:01:41: 2000000 INFO @ Tue, 16 Jun 2020 08:01:42: 6000000 INFO @ Tue, 16 Jun 2020 08:01:49: 3000000 INFO @ Tue, 16 Jun 2020 08:01:51: 7000000 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 08:01:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.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 08:01:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:01:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:01:57: 4000000 INFO @ Tue, 16 Jun 2020 08:01:59: 8000000 INFO @ Tue, 16 Jun 2020 08:02:03: 1000000 INFO @ Tue, 16 Jun 2020 08:02:05: 5000000 INFO @ Tue, 16 Jun 2020 08:02:08: 9000000 INFO @ Tue, 16 Jun 2020 08:02:11: 2000000 INFO @ Tue, 16 Jun 2020 08:02:13: 6000000 INFO @ Tue, 16 Jun 2020 08:02:16: 10000000 INFO @ Tue, 16 Jun 2020 08:02:19: 3000000 INFO @ Tue, 16 Jun 2020 08:02:21: 7000000 INFO @ Tue, 16 Jun 2020 08:02:25: 11000000 INFO @ Tue, 16 Jun 2020 08:02:27: 4000000 INFO @ Tue, 16 Jun 2020 08:02:29: 8000000 INFO @ Tue, 16 Jun 2020 08:02:30: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:02:30: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:02:30: #1 total tags in treatment: 11589881 INFO @ Tue, 16 Jun 2020 08:02:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:30: #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 08:02:30: #1 tags after filtering in treatment: 11589881 INFO @ Tue, 16 Jun 2020 08:02:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:31: #2 number of paired peaks: 137 WARNING @ Tue, 16 Jun 2020 08:02:31: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Tue, 16 Jun 2020 08:02:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:31: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:02:31: #2 alternative fragment length(s) may be 2,10,52,517,554,594 bps INFO @ Tue, 16 Jun 2020 08:02:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.05_model.r WARNING @ Tue, 16 Jun 2020 08:02:31: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:02:31: #2 You may need to consider one of the other alternative d(s): 2,10,52,517,554,594 WARNING @ Tue, 16 Jun 2020 08:02:31: #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 08:02:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:02:35: 5000000 INFO @ Tue, 16 Jun 2020 08:02:37: 9000000 INFO @ Tue, 16 Jun 2020 08:02:42: 6000000 INFO @ Tue, 16 Jun 2020 08:02:44: 10000000 INFO @ Tue, 16 Jun 2020 08:02:50: 7000000 INFO @ Tue, 16 Jun 2020 08:02:52: 11000000 INFO @ Tue, 16 Jun 2020 08:02:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:02:56: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:02:56: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:02:56: #1 total tags in treatment: 11589881 INFO @ Tue, 16 Jun 2020 08:02:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:02:56: #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 08:02:56: #1 tags after filtering in treatment: 11589881 INFO @ Tue, 16 Jun 2020 08:02:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:02:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:02:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:02:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:02:57: 8000000 INFO @ Tue, 16 Jun 2020 08:02:57: #2 number of paired peaks: 137 WARNING @ Tue, 16 Jun 2020 08:02:57: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Tue, 16 Jun 2020 08:02:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:02:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:02:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:02:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:02:57: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:02:57: #2 alternative fragment length(s) may be 2,10,52,517,554,594 bps INFO @ Tue, 16 Jun 2020 08:02:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.10_model.r WARNING @ Tue, 16 Jun 2020 08:02:57: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:02:57: #2 You may need to consider one of the other alternative d(s): 2,10,52,517,554,594 WARNING @ Tue, 16 Jun 2020 08:02:57: #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 08:02:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:02:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:03:03: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:03:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.05_summits.bed INFO @ Tue, 16 Jun 2020 08:03:07: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1071 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:03:10: 10000000 INFO @ Tue, 16 Jun 2020 08:03:16: 11000000 INFO @ Tue, 16 Jun 2020 08:03:20: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:03:20: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:03:20: #1 total tags in treatment: 11589881 INFO @ Tue, 16 Jun 2020 08:03:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:03:20: #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 08:03:20: #1 tags after filtering in treatment: 11589881 INFO @ Tue, 16 Jun 2020 08:03:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:03:20: #1 finished! INFO @ Tue, 16 Jun 2020 08:03:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:03:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:03:20: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:21: #2 number of paired peaks: 137 WARNING @ Tue, 16 Jun 2020 08:03:21: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Tue, 16 Jun 2020 08:03:21: start model_add_line... INFO @ Tue, 16 Jun 2020 08:03:21: start X-correlation... INFO @ Tue, 16 Jun 2020 08:03:21: end of X-cor INFO @ Tue, 16 Jun 2020 08:03:21: #2 finished! INFO @ Tue, 16 Jun 2020 08:03:21: #2 predicted fragment length is 52 bps INFO @ Tue, 16 Jun 2020 08:03:21: #2 alternative fragment length(s) may be 2,10,52,517,554,594 bps INFO @ Tue, 16 Jun 2020 08:03:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.20_model.r WARNING @ Tue, 16 Jun 2020 08:03:21: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:03:21: #2 You may need to consider one of the other alternative d(s): 2,10,52,517,554,594 WARNING @ Tue, 16 Jun 2020 08:03:21: #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 08:03:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:03:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:03:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.10_summits.bed INFO @ Tue, 16 Jun 2020 08:03:31: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (197 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:03:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:03:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:03:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:03:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1132920/SRX1132920.20_summits.bed INFO @ Tue, 16 Jun 2020 08:03:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (17 records, 4 fields): 1 millis CompletedMACS2peakCalling