Job ID = 6368415 SRX = SRX495094 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:11:50 prefetch.2.10.7: 1) Downloading 'SRR1198626'... 2020-06-16T00:11:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:14:26 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:14:27 prefetch.2.10.7: 'SRR1198626' is valid 2020-06-16T00:14:27 prefetch.2.10.7: 1) 'SRR1198626' was downloaded successfully Read 18854814 spots for SRR1198626/SRR1198626.sra Written 18854814 spots for SRR1198626/SRR1198626.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: 00:03:46 18854814 reads; of these: 18854814 (100.00%) were unpaired; of these: 288199 (1.53%) aligned 0 times 14954511 (79.31%) aligned exactly 1 time 3612104 (19.16%) aligned >1 times 98.47% overall alignment rate Time searching: 00:03:46 Overall time: 00:03:46 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] 3522289 / 18566615 = 0.1897 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 09:22:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.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 09:22:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:22:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:05: 1000000 INFO @ Tue, 16 Jun 2020 09:23:10: 2000000 INFO @ Tue, 16 Jun 2020 09:23:15: 3000000 INFO @ Tue, 16 Jun 2020 09:23:20: 4000000 INFO @ Tue, 16 Jun 2020 09:23:26: 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 09:23:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.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 09:23:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:31: 6000000 INFO @ Tue, 16 Jun 2020 09:23:34: 1000000 INFO @ Tue, 16 Jun 2020 09:23:36: 7000000 INFO @ Tue, 16 Jun 2020 09:23:39: 2000000 INFO @ Tue, 16 Jun 2020 09:23:42: 8000000 INFO @ Tue, 16 Jun 2020 09:23:43: 3000000 INFO @ Tue, 16 Jun 2020 09:23:47: 9000000 INFO @ Tue, 16 Jun 2020 09:23:48: 4000000 INFO @ Tue, 16 Jun 2020 09:23:53: 10000000 INFO @ Tue, 16 Jun 2020 09:23:53: 5000000 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 09:23:58: 6000000 INFO @ Tue, 16 Jun 2020 09:23:58: 11000000 INFO @ Tue, 16 Jun 2020 09:23:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.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 09:23:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:03: 7000000 INFO @ Tue, 16 Jun 2020 09:24:03: 12000000 INFO @ Tue, 16 Jun 2020 09:24:05: 1000000 INFO @ Tue, 16 Jun 2020 09:24:07: 8000000 INFO @ Tue, 16 Jun 2020 09:24:09: 13000000 INFO @ Tue, 16 Jun 2020 09:24:10: 2000000 INFO @ Tue, 16 Jun 2020 09:24:12: 9000000 INFO @ Tue, 16 Jun 2020 09:24:15: 14000000 INFO @ Tue, 16 Jun 2020 09:24:16: 3000000 INFO @ Tue, 16 Jun 2020 09:24:17: 10000000 INFO @ Tue, 16 Jun 2020 09:24:20: 15000000 INFO @ Tue, 16 Jun 2020 09:24:21: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:24:21: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:24:21: #1 total tags in treatment: 15044326 INFO @ Tue, 16 Jun 2020 09:24:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:24:21: #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 09:24:21: #1 tags after filtering in treatment: 15044326 INFO @ Tue, 16 Jun 2020 09:24:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:24:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:24:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:24:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:24:21: 4000000 INFO @ Tue, 16 Jun 2020 09:24:22: 11000000 INFO @ Tue, 16 Jun 2020 09:24:22: #2 number of paired peaks: 436 WARNING @ Tue, 16 Jun 2020 09:24:22: Fewer paired peaks (436) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 436 pairs to build model! INFO @ Tue, 16 Jun 2020 09:24:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:24:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:24:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:24:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:24:22: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:24:22: #2 alternative fragment length(s) may be 2,45,597 bps INFO @ Tue, 16 Jun 2020 09:24:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.05_model.r WARNING @ Tue, 16 Jun 2020 09:24:22: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:24:22: #2 You may need to consider one of the other alternative d(s): 2,45,597 WARNING @ Tue, 16 Jun 2020 09:24:22: #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 09:24:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:24:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:24:27: 12000000 INFO @ Tue, 16 Jun 2020 09:24:27: 5000000 INFO @ Tue, 16 Jun 2020 09:24:31: 13000000 INFO @ Tue, 16 Jun 2020 09:24:32: 6000000 INFO @ Tue, 16 Jun 2020 09:24:36: 14000000 INFO @ Tue, 16 Jun 2020 09:24:38: 7000000 INFO @ Tue, 16 Jun 2020 09:24:41: 15000000 INFO @ Tue, 16 Jun 2020 09:24:41: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:24:41: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:24:41: #1 total tags in treatment: 15044326 INFO @ Tue, 16 Jun 2020 09:24:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:24:41: #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 09:24:42: #1 tags after filtering in treatment: 15044326 INFO @ Tue, 16 Jun 2020 09:24:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:24:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:24:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:24:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:24:43: #2 number of paired peaks: 436 WARNING @ Tue, 16 Jun 2020 09:24:43: Fewer paired peaks (436) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 436 pairs to build model! INFO @ Tue, 16 Jun 2020 09:24:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:24:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:24:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:24:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:24:43: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:24:43: #2 alternative fragment length(s) may be 2,45,597 bps INFO @ Tue, 16 Jun 2020 09:24:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.10_model.r WARNING @ Tue, 16 Jun 2020 09:24:43: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:24:43: #2 You may need to consider one of the other alternative d(s): 2,45,597 WARNING @ Tue, 16 Jun 2020 09:24:43: #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 09:24:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:24:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:24:43: 8000000 INFO @ Tue, 16 Jun 2020 09:24:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:24:49: 9000000 INFO @ Tue, 16 Jun 2020 09:24:54: 10000000 INFO @ Tue, 16 Jun 2020 09:24:59: 11000000 INFO @ Tue, 16 Jun 2020 09:25:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:25:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:25:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.05_summits.bed INFO @ Tue, 16 Jun 2020 09:25:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3846 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:25:05: 12000000 INFO @ Tue, 16 Jun 2020 09:25:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:25:10: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:25:16: 14000000 INFO @ Tue, 16 Jun 2020 09:25:21: 15000000 INFO @ Tue, 16 Jun 2020 09:25:21: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:25:21: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:25:21: #1 total tags in treatment: 15044326 INFO @ Tue, 16 Jun 2020 09:25:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:21: #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 09:25:22: #1 tags after filtering in treatment: 15044326 INFO @ Tue, 16 Jun 2020 09:25:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:25:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:23: #2 number of paired peaks: 436 WARNING @ Tue, 16 Jun 2020 09:25:23: Fewer paired peaks (436) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 436 pairs to build model! INFO @ Tue, 16 Jun 2020 09:25:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:23: #2 predicted fragment length is 45 bps INFO @ Tue, 16 Jun 2020 09:25:23: #2 alternative fragment length(s) may be 2,45,597 bps INFO @ Tue, 16 Jun 2020 09:25:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.20_model.r WARNING @ Tue, 16 Jun 2020 09:25:23: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:25:23: #2 You may need to consider one of the other alternative d(s): 2,45,597 WARNING @ Tue, 16 Jun 2020 09:25:23: #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 09:25:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:25:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:25:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:25:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.10_summits.bed INFO @ Tue, 16 Jun 2020 09:25:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (938 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:25:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495094/SRX495094.20_summits.bed INFO @ Tue, 16 Jun 2020 09:26:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (263 records, 4 fields): 1 millis CompletedMACS2peakCalling