Job ID = 8069422 SRX = SRX8392417 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:32:29 prefetch.2.10.7: 1) Downloading 'SRR11842070'... 2020-08-08T03:32:29 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:34:06 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:34:06 prefetch.2.10.7: 1) 'SRR11842070' was downloaded successfully 2020-08-08T03:34:06 prefetch.2.10.7: 'SRR11842070' has 0 unresolved dependencies Read 8367369 spots for SRR11842070/SRR11842070.sra Written 8367369 spots for SRR11842070/SRR11842070.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070372 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:36 8367369 reads; of these: 8367369 (100.00%) were paired; of these: 1435126 (17.15%) aligned concordantly 0 times 6060375 (72.43%) aligned concordantly exactly 1 time 871868 (10.42%) aligned concordantly >1 times ---- 1435126 pairs aligned concordantly 0 times; of these: 559776 (39.01%) aligned discordantly 1 time ---- 875350 pairs aligned 0 times concordantly or discordantly; of these: 1750700 mates make up the pairs; of these: 1528791 (87.32%) aligned 0 times 98230 (5.61%) aligned exactly 1 time 123679 (7.06%) aligned >1 times 90.86% overall alignment rate Time searching: 00:14:37 Overall time: 00:14:37 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 1708775 / 7450113 = 0.2294 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 @ Sat, 08 Aug 2020 12:55:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.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 @ Sat, 08 Aug 2020 12:55:31: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:55:31: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:55:41: 1000000 INFO @ Sat, 08 Aug 2020 12:55:51: 2000000 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 @ Sat, 08 Aug 2020 12:56:00: 3000000 INFO @ Sat, 08 Aug 2020 12:56:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.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 @ Sat, 08 Aug 2020 12:56:02: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:56:02: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:56:11: 4000000 INFO @ Sat, 08 Aug 2020 12:56:13: 1000000 INFO @ Sat, 08 Aug 2020 12:56:23: 5000000 INFO @ Sat, 08 Aug 2020 12:56:25: 2000000 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 @ Sat, 08 Aug 2020 12:56:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.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 @ Sat, 08 Aug 2020 12:56:31: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:56:31: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:56:34: 6000000 INFO @ Sat, 08 Aug 2020 12:56:36: 3000000 INFO @ Sat, 08 Aug 2020 12:56:44: 1000000 INFO @ Sat, 08 Aug 2020 12:56:46: 7000000 INFO @ Sat, 08 Aug 2020 12:56:48: 4000000 INFO @ Sat, 08 Aug 2020 12:56:57: 2000000 INFO @ Sat, 08 Aug 2020 12:56:57: 8000000 INFO @ Sat, 08 Aug 2020 12:57:00: 5000000 INFO @ Sat, 08 Aug 2020 12:57:09: 9000000 INFO @ Sat, 08 Aug 2020 12:57:10: 3000000 INFO @ Sat, 08 Aug 2020 12:57:12: 6000000 INFO @ Sat, 08 Aug 2020 12:57:21: 10000000 INFO @ Sat, 08 Aug 2020 12:57:22: 4000000 INFO @ Sat, 08 Aug 2020 12:57:23: 7000000 INFO @ Sat, 08 Aug 2020 12:57:33: 11000000 INFO @ Sat, 08 Aug 2020 12:57:33: 5000000 INFO @ Sat, 08 Aug 2020 12:57:35: 8000000 INFO @ Sat, 08 Aug 2020 12:57:42: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:57:42: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:57:42: #1 total tags in treatment: 5296516 INFO @ Sat, 08 Aug 2020 12:57:42: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:57:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:57:42: #1 tags after filtering in treatment: 4779079 INFO @ Sat, 08 Aug 2020 12:57:42: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 12:57:42: #1 finished! INFO @ Sat, 08 Aug 2020 12:57:42: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:57:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:57:42: #2 number of paired peaks: 1034 INFO @ Sat, 08 Aug 2020 12:57:42: start model_add_line... INFO @ Sat, 08 Aug 2020 12:57:42: start X-correlation... INFO @ Sat, 08 Aug 2020 12:57:42: end of X-cor INFO @ Sat, 08 Aug 2020 12:57:42: #2 finished! INFO @ Sat, 08 Aug 2020 12:57:42: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 12:57:42: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 08 Aug 2020 12:57:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.05_model.r WARNING @ Sat, 08 Aug 2020 12:57:42: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:57:42: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Sat, 08 Aug 2020 12:57:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:57:42: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:57:42: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:57:45: 6000000 INFO @ Sat, 08 Aug 2020 12:57:47: 9000000 INFO @ Sat, 08 Aug 2020 12:57:53: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:57:57: 7000000 INFO @ Sat, 08 Aug 2020 12:57:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:57:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:57:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.05_summits.bed INFO @ Sat, 08 Aug 2020 12:57:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5243 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:57:59: 10000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:58:09: 8000000 INFO @ Sat, 08 Aug 2020 12:58:11: 11000000 INFO @ Sat, 08 Aug 2020 12:58:19: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:58:19: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:58:19: #1 total tags in treatment: 5296516 INFO @ Sat, 08 Aug 2020 12:58:19: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:58:20: #1 tags after filtering in treatment: 4779079 INFO @ Sat, 08 Aug 2020 12:58:20: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 12:58:20: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:20: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:20: #2 number of paired peaks: 1034 INFO @ Sat, 08 Aug 2020 12:58:20: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:20: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:20: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:20: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:20: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 12:58:20: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 08 Aug 2020 12:58:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.10_model.r WARNING @ Sat, 08 Aug 2020 12:58:20: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:58:20: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Sat, 08 Aug 2020 12:58:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:58:20: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:58:20: 9000000 INFO @ Sat, 08 Aug 2020 12:58:30: 10000000 INFO @ Sat, 08 Aug 2020 12:58:31: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:58:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:58:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:58:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.10_summits.bed INFO @ Sat, 08 Aug 2020 12:58:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2690 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:58:40: 11000000 INFO @ Sat, 08 Aug 2020 12:58:48: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:58:48: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:58:48: #1 total tags in treatment: 5296516 INFO @ Sat, 08 Aug 2020 12:58:48: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:58:48: #1 tags after filtering in treatment: 4779079 INFO @ Sat, 08 Aug 2020 12:58:48: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 12:58:48: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:48: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:48: #2 number of paired peaks: 1034 INFO @ Sat, 08 Aug 2020 12:58:48: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:48: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:48: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:48: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:48: #2 predicted fragment length is 203 bps INFO @ Sat, 08 Aug 2020 12:58:48: #2 alternative fragment length(s) may be 203 bps INFO @ Sat, 08 Aug 2020 12:58:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.20_model.r WARNING @ Sat, 08 Aug 2020 12:58:48: #2 Since the d (203) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:58:48: #2 You may need to consider one of the other alternative d(s): 203 WARNING @ Sat, 08 Aug 2020 12:58:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:58:48: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:58:59: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:59:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:59:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:59:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392417/SRX8392417.20_summits.bed INFO @ Sat, 08 Aug 2020 12:59:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1006 records, 4 fields): 2 millis CompletedMACS2peakCalling