Job ID = 8069404 SRX = SRX7217792 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:32:14 prefetch.2.10.7: 1) Downloading 'SRR10533869'... 2020-08-08T03:32:14 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:37:07 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:37:07 prefetch.2.10.7: 1) 'SRR10533869' was downloaded successfully 2020-08-08T03:37:07 prefetch.2.10.7: 'SRR10533869' has 0 unresolved dependencies Read 8412168 spots for SRR10533869/SRR10533869.sra Written 8412168 spots for SRR10533869/SRR10533869.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070555 ("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: 00:15:16 8412168 reads; of these: 8412168 (100.00%) were paired; of these: 997922 (11.86%) aligned concordantly 0 times 6550337 (77.87%) aligned concordantly exactly 1 time 863909 (10.27%) aligned concordantly >1 times ---- 997922 pairs aligned concordantly 0 times; of these: 416028 (41.69%) aligned discordantly 1 time ---- 581894 pairs aligned 0 times concordantly or discordantly; of these: 1163788 mates make up the pairs; of these: 953978 (81.97%) aligned 0 times 109590 (9.42%) aligned exactly 1 time 100220 (8.61%) aligned >1 times 94.33% overall alignment rate Time searching: 00:15:16 Overall time: 00:15:16 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] 2167460 / 7796879 = 0.2780 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 12:59:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.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 12:59:12: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:59:12: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:59:18: 1000000 INFO @ Sat, 08 Aug 2020 12:59:24: 2000000 INFO @ Sat, 08 Aug 2020 12:59:31: 3000000 INFO @ Sat, 08 Aug 2020 12:59:37: 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 @ Sat, 08 Aug 2020 12:59:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.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 12:59:42: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:59:42: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:59:43: 5000000 INFO @ Sat, 08 Aug 2020 12:59:48: 1000000 INFO @ Sat, 08 Aug 2020 12:59:49: 6000000 INFO @ Sat, 08 Aug 2020 12:59:54: 2000000 INFO @ Sat, 08 Aug 2020 12:59:56: 7000000 INFO @ Sat, 08 Aug 2020 13:00:01: 3000000 INFO @ Sat, 08 Aug 2020 13:00:02: 8000000 INFO @ Sat, 08 Aug 2020 13:00:07: 4000000 INFO @ Sat, 08 Aug 2020 13:00:08: 9000000 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 13:00:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.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 13:00:12: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:00:12: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:00:13: 5000000 INFO @ Sat, 08 Aug 2020 13:00:14: 10000000 INFO @ Sat, 08 Aug 2020 13:00:19: 1000000 INFO @ Sat, 08 Aug 2020 13:00:19: 6000000 INFO @ Sat, 08 Aug 2020 13:00:21: 11000000 INFO @ Sat, 08 Aug 2020 13:00:24: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:00:24: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:00:24: #1 total tags in treatment: 5303365 INFO @ Sat, 08 Aug 2020 13:00:24: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:00:24: #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 13:00:24: #1 tags after filtering in treatment: 4784201 INFO @ Sat, 08 Aug 2020 13:00:24: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:00:24: #1 finished! INFO @ Sat, 08 Aug 2020 13:00:24: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:00:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:00:25: #2 number of paired peaks: 1236 INFO @ Sat, 08 Aug 2020 13:00:25: start model_add_line... INFO @ Sat, 08 Aug 2020 13:00:25: start X-correlation... INFO @ Sat, 08 Aug 2020 13:00:25: end of X-cor INFO @ Sat, 08 Aug 2020 13:00:25: #2 finished! INFO @ Sat, 08 Aug 2020 13:00:25: #2 predicted fragment length is 217 bps INFO @ Sat, 08 Aug 2020 13:00:25: #2 alternative fragment length(s) may be 217 bps INFO @ Sat, 08 Aug 2020 13:00:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.05_model.r WARNING @ Sat, 08 Aug 2020 13:00:25: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:00:25: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Sat, 08 Aug 2020 13:00:25: #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 13:00:25: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:00:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:00:26: 7000000 INFO @ Sat, 08 Aug 2020 13:00:27: 2000000 INFO @ Sat, 08 Aug 2020 13:00:32: 8000000 INFO @ Sat, 08 Aug 2020 13:00:35: 3000000 INFO @ Sat, 08 Aug 2020 13:00:36: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:00:38: 9000000 INFO @ Sat, 08 Aug 2020 13:00:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:00:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:00:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.05_summits.bed INFO @ Sat, 08 Aug 2020 13:00:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (5395 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:00:43: 4000000 INFO @ Sat, 08 Aug 2020 13:00:45: 10000000 INFO @ Sat, 08 Aug 2020 13:00:51: 5000000 INFO @ Sat, 08 Aug 2020 13:00:51: 11000000 INFO @ Sat, 08 Aug 2020 13:00:54: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:00:54: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:00:54: #1 total tags in treatment: 5303365 INFO @ Sat, 08 Aug 2020 13:00:54: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:00:54: #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 13:00:55: #1 tags after filtering in treatment: 4784201 INFO @ Sat, 08 Aug 2020 13:00:55: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:00:55: #1 finished! INFO @ Sat, 08 Aug 2020 13:00:55: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:00:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:00:55: #2 number of paired peaks: 1236 INFO @ Sat, 08 Aug 2020 13:00:55: start model_add_line... INFO @ Sat, 08 Aug 2020 13:00:55: start X-correlation... INFO @ Sat, 08 Aug 2020 13:00:55: end of X-cor INFO @ Sat, 08 Aug 2020 13:00:55: #2 finished! INFO @ Sat, 08 Aug 2020 13:00:55: #2 predicted fragment length is 217 bps INFO @ Sat, 08 Aug 2020 13:00:55: #2 alternative fragment length(s) may be 217 bps INFO @ Sat, 08 Aug 2020 13:00:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.10_model.r WARNING @ Sat, 08 Aug 2020 13:00:55: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:00:55: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Sat, 08 Aug 2020 13:00:55: #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 13:00:55: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:00:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:00:59: 6000000 INFO @ Sat, 08 Aug 2020 13:01:06: 7000000 INFO @ Sat, 08 Aug 2020 13:01:06: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:01:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:01:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:01:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.10_summits.bed INFO @ Sat, 08 Aug 2020 13:01:12: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2962 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:01:14: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:01:21: 9000000 INFO @ Sat, 08 Aug 2020 13:01:29: 10000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:01:36: 11000000 INFO @ Sat, 08 Aug 2020 13:01:41: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:01:41: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:01:41: #1 total tags in treatment: 5303365 INFO @ Sat, 08 Aug 2020 13:01:41: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:01:41: #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 13:01:41: #1 tags after filtering in treatment: 4784201 INFO @ Sat, 08 Aug 2020 13:01:41: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:01:41: #1 finished! INFO @ Sat, 08 Aug 2020 13:01:41: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:01:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:01:41: #2 number of paired peaks: 1236 INFO @ Sat, 08 Aug 2020 13:01:41: start model_add_line... INFO @ Sat, 08 Aug 2020 13:01:41: start X-correlation... INFO @ Sat, 08 Aug 2020 13:01:41: end of X-cor INFO @ Sat, 08 Aug 2020 13:01:41: #2 finished! INFO @ Sat, 08 Aug 2020 13:01:41: #2 predicted fragment length is 217 bps INFO @ Sat, 08 Aug 2020 13:01:41: #2 alternative fragment length(s) may be 217 bps INFO @ Sat, 08 Aug 2020 13:01:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.20_model.r WARNING @ Sat, 08 Aug 2020 13:01:41: #2 Since the d (217) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:01:41: #2 You may need to consider one of the other alternative d(s): 217 WARNING @ Sat, 08 Aug 2020 13:01:41: #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 13:01:41: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:01:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:01:52: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:01:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:01:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:01:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217792/SRX7217792.20_summits.bed INFO @ Sat, 08 Aug 2020 13:01:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1146 records, 4 fields): 3 millis CompletedMACS2peakCalling