Job ID = 8069429 SRX = SRX8392419 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 'SRR11842072'... 2020-08-08T03:32:29 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:34:47 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:34:47 prefetch.2.10.7: 1) 'SRR11842072' was downloaded successfully 2020-08-08T03:34:47 prefetch.2.10.7: 'SRR11842072' has 0 unresolved dependencies Read 8473861 spots for SRR11842072/SRR11842072.sra Written 8473861 spots for SRR11842072/SRR11842072.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070394 ("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: 00:14:23 8473861 reads; of these: 8473861 (100.00%) were paired; of these: 1554101 (18.34%) aligned concordantly 0 times 6159595 (72.69%) aligned concordantly exactly 1 time 760165 (8.97%) aligned concordantly >1 times ---- 1554101 pairs aligned concordantly 0 times; of these: 728287 (46.86%) aligned discordantly 1 time ---- 825814 pairs aligned 0 times concordantly or discordantly; of these: 1651628 mates make up the pairs; of these: 1418443 (85.88%) aligned 0 times 96917 (5.87%) aligned exactly 1 time 136268 (8.25%) aligned >1 times 91.63% overall alignment rate Time searching: 00:14:23 Overall time: 00:14:23 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] 1462836 / 7601132 = 0.1924 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 12:56:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.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 12:56:07: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:56:07: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:56:17: 1000000 INFO @ Sat, 08 Aug 2020 12:56:26: 2000000 INFO @ Sat, 08 Aug 2020 12:56:34: 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 @ Sat, 08 Aug 2020 12:56:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.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 12:56:38: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:56:38: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:56:43: 4000000 INFO @ Sat, 08 Aug 2020 12:56:48: 1000000 INFO @ Sat, 08 Aug 2020 12:56:52: 5000000 INFO @ Sat, 08 Aug 2020 12:56:59: 2000000 INFO @ Sat, 08 Aug 2020 12:57:01: 6000000 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 12:57:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.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 12:57:07: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:57:07: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:57:10: 3000000 INFO @ Sat, 08 Aug 2020 12:57:11: 7000000 INFO @ Sat, 08 Aug 2020 12:57:18: 1000000 INFO @ Sat, 08 Aug 2020 12:57:20: 4000000 INFO @ Sat, 08 Aug 2020 12:57:21: 8000000 INFO @ Sat, 08 Aug 2020 12:57:29: 2000000 INFO @ Sat, 08 Aug 2020 12:57:31: 5000000 INFO @ Sat, 08 Aug 2020 12:57:31: 9000000 INFO @ Sat, 08 Aug 2020 12:57:39: 3000000 INFO @ Sat, 08 Aug 2020 12:57:41: 10000000 INFO @ Sat, 08 Aug 2020 12:57:41: 6000000 INFO @ Sat, 08 Aug 2020 12:57:50: 4000000 INFO @ Sat, 08 Aug 2020 12:57:52: 11000000 INFO @ Sat, 08 Aug 2020 12:57:52: 7000000 INFO @ Sat, 08 Aug 2020 12:58:00: 5000000 INFO @ Sat, 08 Aug 2020 12:58:02: 12000000 INFO @ Sat, 08 Aug 2020 12:58:02: 8000000 INFO @ Sat, 08 Aug 2020 12:58:08: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:58:08: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:58:08: #1 total tags in treatment: 5549470 INFO @ Sat, 08 Aug 2020 12:58:08: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:08: #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 12:58:08: #1 tags after filtering in treatment: 4960484 INFO @ Sat, 08 Aug 2020 12:58:08: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 12:58:08: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:08: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:09: #2 number of paired peaks: 2045 INFO @ Sat, 08 Aug 2020 12:58:09: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:09: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:09: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:09: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:09: #2 predicted fragment length is 204 bps INFO @ Sat, 08 Aug 2020 12:58:09: #2 alternative fragment length(s) may be 204 bps INFO @ Sat, 08 Aug 2020 12:58:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.05_model.r WARNING @ Sat, 08 Aug 2020 12:58:09: #2 Since the d (204) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:58:09: #2 You may need to consider one of the other alternative d(s): 204 WARNING @ Sat, 08 Aug 2020 12:58:09: #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 12:58:09: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:58:10: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:58:13: 9000000 INFO @ Sat, 08 Aug 2020 12:58:21: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:58:21: 7000000 INFO @ Sat, 08 Aug 2020 12:58:23: 10000000 INFO @ Sat, 08 Aug 2020 12:58:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:58:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:58:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.05_summits.bed INFO @ Sat, 08 Aug 2020 12:58:26: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7804 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:58:31: 8000000 INFO @ Sat, 08 Aug 2020 12:58:33: 11000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:58:42: 9000000 INFO @ Sat, 08 Aug 2020 12:58:44: 12000000 INFO @ Sat, 08 Aug 2020 12:58:50: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:58:50: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:58:50: #1 total tags in treatment: 5549470 INFO @ Sat, 08 Aug 2020 12:58:50: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:50: #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 12:58:50: #1 tags after filtering in treatment: 4960484 INFO @ Sat, 08 Aug 2020 12:58:50: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 12:58:50: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:50: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:50: #2 number of paired peaks: 2045 INFO @ Sat, 08 Aug 2020 12:58:50: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:50: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:50: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:50: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:50: #2 predicted fragment length is 204 bps INFO @ Sat, 08 Aug 2020 12:58:50: #2 alternative fragment length(s) may be 204 bps INFO @ Sat, 08 Aug 2020 12:58:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.10_model.r WARNING @ Sat, 08 Aug 2020 12:58:50: #2 Since the d (204) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:58:50: #2 You may need to consider one of the other alternative d(s): 204 WARNING @ Sat, 08 Aug 2020 12:58:50: #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 12:58:50: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:58:52: 10000000 INFO @ Sat, 08 Aug 2020 12:59:01: 11000000 INFO @ Sat, 08 Aug 2020 12:59:02: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:59:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:59:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:59:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.10_summits.bed INFO @ Sat, 08 Aug 2020 12:59:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4965 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:59:09: 12000000 INFO @ Sat, 08 Aug 2020 12:59:14: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:59:14: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:59:14: #1 total tags in treatment: 5549470 INFO @ Sat, 08 Aug 2020 12:59:14: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:59:14: #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 12:59:14: #1 tags after filtering in treatment: 4960484 INFO @ Sat, 08 Aug 2020 12:59:14: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 12:59:14: #1 finished! INFO @ Sat, 08 Aug 2020 12:59:14: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:59:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:59:15: #2 number of paired peaks: 2045 INFO @ Sat, 08 Aug 2020 12:59:15: start model_add_line... INFO @ Sat, 08 Aug 2020 12:59:15: start X-correlation... INFO @ Sat, 08 Aug 2020 12:59:15: end of X-cor INFO @ Sat, 08 Aug 2020 12:59:15: #2 finished! INFO @ Sat, 08 Aug 2020 12:59:15: #2 predicted fragment length is 204 bps INFO @ Sat, 08 Aug 2020 12:59:15: #2 alternative fragment length(s) may be 204 bps INFO @ Sat, 08 Aug 2020 12:59:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.20_model.r WARNING @ Sat, 08 Aug 2020 12:59:15: #2 Since the d (204) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:59:15: #2 You may need to consider one of the other alternative d(s): 204 WARNING @ Sat, 08 Aug 2020 12:59:15: #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 12:59:15: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:59:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:59:26: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:59:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:59:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:59:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392419/SRX8392419.20_summits.bed INFO @ Sat, 08 Aug 2020 12:59:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2258 records, 4 fields): 3 millis CompletedMACS2peakCalling