Job ID = 6368815 SRX = SRX5985669 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:27:35 prefetch.2.10.7: 1) Downloading 'SRR9214974'... 2020-06-16T00:27:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:35:55 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:35:55 prefetch.2.10.7: 1) 'SRR9214974' was downloaded successfully Read 32679048 spots for SRR9214974/SRR9214974.sra Written 32679048 spots for SRR9214974/SRR9214974.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: 00:05:54 32679048 reads; of these: 32679048 (100.00%) were unpaired; of these: 20156518 (61.68%) aligned 0 times 10448005 (31.97%) aligned exactly 1 time 2074525 (6.35%) aligned >1 times 38.32% overall alignment rate Time searching: 00:05:54 Overall time: 00:05:54 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] 915565 / 12522530 = 0.0731 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 09:48:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.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 09:48:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:34: 1000000 INFO @ Tue, 16 Jun 2020 09:48:40: 2000000 INFO @ Tue, 16 Jun 2020 09:48:46: 3000000 INFO @ Tue, 16 Jun 2020 09:48:53: 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 09:48:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.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 09:48:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:48:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:48:59: 5000000 INFO @ Tue, 16 Jun 2020 09:49:05: 1000000 INFO @ Tue, 16 Jun 2020 09:49:07: 6000000 INFO @ Tue, 16 Jun 2020 09:49:13: 2000000 INFO @ Tue, 16 Jun 2020 09:49:14: 7000000 INFO @ Tue, 16 Jun 2020 09:49:20: 3000000 INFO @ Tue, 16 Jun 2020 09:49:22: 8000000 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 09:49:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.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 09:49:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:28: 4000000 INFO @ Tue, 16 Jun 2020 09:49:29: 9000000 INFO @ Tue, 16 Jun 2020 09:49:35: 1000000 INFO @ Tue, 16 Jun 2020 09:49:35: 5000000 INFO @ Tue, 16 Jun 2020 09:49:37: 10000000 INFO @ Tue, 16 Jun 2020 09:49:42: 2000000 INFO @ Tue, 16 Jun 2020 09:49:43: 6000000 INFO @ Tue, 16 Jun 2020 09:49:44: 11000000 INFO @ Tue, 16 Jun 2020 09:49:48: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:49:48: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:49:48: #1 total tags in treatment: 11606965 INFO @ Tue, 16 Jun 2020 09:49:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:48: #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 09:49:49: #1 tags after filtering in treatment: 11606965 INFO @ Tue, 16 Jun 2020 09:49:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:49:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:49: #2 number of paired peaks: 306 WARNING @ Tue, 16 Jun 2020 09:49:49: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Tue, 16 Jun 2020 09:49:49: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:49: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:49: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:49: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:49: #2 predicted fragment length is 72 bps INFO @ Tue, 16 Jun 2020 09:49:49: #2 alternative fragment length(s) may be 3,72 bps INFO @ Tue, 16 Jun 2020 09:49:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.05_model.r WARNING @ Tue, 16 Jun 2020 09:49:49: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:49:49: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Tue, 16 Jun 2020 09:49:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:49:49: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:50: 3000000 INFO @ Tue, 16 Jun 2020 09:49:50: 7000000 INFO @ Tue, 16 Jun 2020 09:49:57: 8000000 INFO @ Tue, 16 Jun 2020 09:49:57: 4000000 INFO @ Tue, 16 Jun 2020 09:50:04: 9000000 INFO @ Tue, 16 Jun 2020 09:50:04: 5000000 INFO @ Tue, 16 Jun 2020 09:50:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:11: 10000000 INFO @ Tue, 16 Jun 2020 09:50:12: 6000000 INFO @ Tue, 16 Jun 2020 09:50:19: 11000000 INFO @ Tue, 16 Jun 2020 09:50:19: 7000000 INFO @ Tue, 16 Jun 2020 09:50:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.05_summits.bed INFO @ Tue, 16 Jun 2020 09:50:20: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (532 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:50:23: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:50:23: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:50:23: #1 total tags in treatment: 11606965 INFO @ Tue, 16 Jun 2020 09:50:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:23: #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 09:50:23: #1 tags after filtering in treatment: 11606965 INFO @ Tue, 16 Jun 2020 09:50:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:24: #2 number of paired peaks: 306 WARNING @ Tue, 16 Jun 2020 09:50:24: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Tue, 16 Jun 2020 09:50:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:24: #2 predicted fragment length is 72 bps INFO @ Tue, 16 Jun 2020 09:50:24: #2 alternative fragment length(s) may be 3,72 bps INFO @ Tue, 16 Jun 2020 09:50:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.10_model.r WARNING @ Tue, 16 Jun 2020 09:50:24: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:50:24: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Tue, 16 Jun 2020 09:50:24: #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 09:50:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:24: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:50:26: 8000000 INFO @ Tue, 16 Jun 2020 09:50:33: 9000000 INFO @ Tue, 16 Jun 2020 09:50:39: 10000000 INFO @ Tue, 16 Jun 2020 09:50:45: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:45: 11000000 INFO @ Tue, 16 Jun 2020 09:50:49: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:50:49: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:50:49: #1 total tags in treatment: 11606965 INFO @ Tue, 16 Jun 2020 09:50:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:49: #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 09:50:49: #1 tags after filtering in treatment: 11606965 INFO @ Tue, 16 Jun 2020 09:50:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:50:50: #2 number of paired peaks: 306 WARNING @ Tue, 16 Jun 2020 09:50:50: Fewer paired peaks (306) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 306 pairs to build model! INFO @ Tue, 16 Jun 2020 09:50:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:50:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:50:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:50:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:50:50: #2 predicted fragment length is 72 bps INFO @ Tue, 16 Jun 2020 09:50:50: #2 alternative fragment length(s) may be 3,72 bps INFO @ Tue, 16 Jun 2020 09:50:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.20_model.r WARNING @ Tue, 16 Jun 2020 09:50:50: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:50:50: #2 You may need to consider one of the other alternative d(s): 3,72 WARNING @ Tue, 16 Jun 2020 09:50:50: #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 09:50:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:50:50: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:50:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.10_summits.bed INFO @ Tue, 16 Jun 2020 09:50:56: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (414 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:51:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:51:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:51:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:51:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5985669/SRX5985669.20_summits.bed INFO @ Tue, 16 Jun 2020 09:51:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (232 records, 4 fields): 2 millis CompletedMACS2peakCalling