Job ID = 6497356 SRX = SRX2011724 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:23:44 prefetch.2.10.7: 1) Downloading 'SRR4017966'... 2020-06-25T22:23:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:30:45 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:30:45 prefetch.2.10.7: 1) 'SRR4017966' was downloaded successfully Read 12623036 spots for SRR4017966/SRR4017966.sra Written 12623036 spots for SRR4017966/SRR4017966.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: 00:00:01 Multiseed full-index search: 00:18:40 12623036 reads; of these: 12623036 (100.00%) were paired; of these: 1290751 (10.23%) aligned concordantly 0 times 9230165 (73.12%) aligned concordantly exactly 1 time 2102120 (16.65%) aligned concordantly >1 times ---- 1290751 pairs aligned concordantly 0 times; of these: 540078 (41.84%) aligned discordantly 1 time ---- 750673 pairs aligned 0 times concordantly or discordantly; of these: 1501346 mates make up the pairs; of these: 1193839 (79.52%) aligned 0 times 101467 (6.76%) aligned exactly 1 time 206040 (13.72%) aligned >1 times 95.27% overall alignment rate Time searching: 00:18:41 Overall time: 00:18:41 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] 5153897 / 11840339 = 0.4353 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 @ Fri, 26 Jun 2020 08:00:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.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 @ Fri, 26 Jun 2020 08:00:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:00:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:00:17: 1000000 INFO @ Fri, 26 Jun 2020 08:00:24: 2000000 INFO @ Fri, 26 Jun 2020 08:00:31: 3000000 INFO @ Fri, 26 Jun 2020 08:00:38: 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 @ Fri, 26 Jun 2020 08:00:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.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 @ Fri, 26 Jun 2020 08:00:41: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:00:41: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:00:45: 5000000 INFO @ Fri, 26 Jun 2020 08:00:50: 1000000 INFO @ Fri, 26 Jun 2020 08:00:53: 6000000 INFO @ Fri, 26 Jun 2020 08:00:58: 2000000 INFO @ Fri, 26 Jun 2020 08:01:01: 7000000 INFO @ Fri, 26 Jun 2020 08:01:07: 3000000 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 @ Fri, 26 Jun 2020 08:01:09: 8000000 INFO @ Fri, 26 Jun 2020 08:01:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.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 @ Fri, 26 Jun 2020 08:01:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:01:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:01:16: 4000000 INFO @ Fri, 26 Jun 2020 08:01:16: 9000000 INFO @ Fri, 26 Jun 2020 08:01:18: 1000000 INFO @ Fri, 26 Jun 2020 08:01:24: 5000000 INFO @ Fri, 26 Jun 2020 08:01:24: 10000000 INFO @ Fri, 26 Jun 2020 08:01:26: 2000000 INFO @ Fri, 26 Jun 2020 08:01:32: 11000000 INFO @ Fri, 26 Jun 2020 08:01:33: 6000000 INFO @ Fri, 26 Jun 2020 08:01:34: 3000000 INFO @ Fri, 26 Jun 2020 08:01:40: 12000000 INFO @ Fri, 26 Jun 2020 08:01:41: 7000000 INFO @ Fri, 26 Jun 2020 08:01:42: 4000000 INFO @ Fri, 26 Jun 2020 08:01:48: 13000000 INFO @ Fri, 26 Jun 2020 08:01:50: 8000000 INFO @ Fri, 26 Jun 2020 08:01:50: 5000000 INFO @ Fri, 26 Jun 2020 08:01:54: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 08:01:54: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 08:01:54: #1 total tags in treatment: 6340381 INFO @ Fri, 26 Jun 2020 08:01:54: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:01:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:01:54: #1 tags after filtering in treatment: 5406379 INFO @ Fri, 26 Jun 2020 08:01:54: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 26 Jun 2020 08:01:54: #1 finished! INFO @ Fri, 26 Jun 2020 08:01:54: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:01:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:01:55: #2 number of paired peaks: 1746 INFO @ Fri, 26 Jun 2020 08:01:55: start model_add_line... INFO @ Fri, 26 Jun 2020 08:01:55: start X-correlation... INFO @ Fri, 26 Jun 2020 08:01:55: end of X-cor INFO @ Fri, 26 Jun 2020 08:01:55: #2 finished! INFO @ Fri, 26 Jun 2020 08:01:55: #2 predicted fragment length is 186 bps INFO @ Fri, 26 Jun 2020 08:01:55: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 26 Jun 2020 08:01:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.05_model.r WARNING @ Fri, 26 Jun 2020 08:01:55: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:01:55: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Fri, 26 Jun 2020 08:01:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:01:55: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:01:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:01:58: 9000000 INFO @ Fri, 26 Jun 2020 08:01:58: 6000000 INFO @ Fri, 26 Jun 2020 08:02:06: 7000000 INFO @ Fri, 26 Jun 2020 08:02:07: 10000000 INFO @ Fri, 26 Jun 2020 08:02:11: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:02:14: 8000000 INFO @ Fri, 26 Jun 2020 08:02:15: 11000000 INFO @ Fri, 26 Jun 2020 08:02:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:02:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:02:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.05_summits.bed INFO @ Fri, 26 Jun 2020 08:02:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2516 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:02:22: 9000000 INFO @ Fri, 26 Jun 2020 08:02:24: 12000000 INFO @ Fri, 26 Jun 2020 08:02:30: 10000000 INFO @ Fri, 26 Jun 2020 08:02:33: 13000000 INFO @ Fri, 26 Jun 2020 08:02:38: 11000000 INFO @ Fri, 26 Jun 2020 08:02:39: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 08:02:39: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 08:02:39: #1 total tags in treatment: 6340381 INFO @ Fri, 26 Jun 2020 08:02:39: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:02:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:02:39: #1 tags after filtering in treatment: 5406379 INFO @ Fri, 26 Jun 2020 08:02:39: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 26 Jun 2020 08:02:39: #1 finished! INFO @ Fri, 26 Jun 2020 08:02:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:02:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:02:40: #2 number of paired peaks: 1746 INFO @ Fri, 26 Jun 2020 08:02:40: start model_add_line... INFO @ Fri, 26 Jun 2020 08:02:40: start X-correlation... INFO @ Fri, 26 Jun 2020 08:02:40: end of X-cor INFO @ Fri, 26 Jun 2020 08:02:40: #2 finished! INFO @ Fri, 26 Jun 2020 08:02:40: #2 predicted fragment length is 186 bps INFO @ Fri, 26 Jun 2020 08:02:40: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 26 Jun 2020 08:02:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.10_model.r WARNING @ Fri, 26 Jun 2020 08:02:40: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:02:40: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Fri, 26 Jun 2020 08:02:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:02:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:02:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:02:45: 12000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:02:52: 13000000 INFO @ Fri, 26 Jun 2020 08:02:56: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:02:58: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 08:02:58: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 08:02:58: #1 total tags in treatment: 6340381 INFO @ Fri, 26 Jun 2020 08:02:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:02:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:02:58: #1 tags after filtering in treatment: 5406379 INFO @ Fri, 26 Jun 2020 08:02:58: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 26 Jun 2020 08:02:58: #1 finished! INFO @ Fri, 26 Jun 2020 08:02:58: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:02:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:02:58: #2 number of paired peaks: 1746 INFO @ Fri, 26 Jun 2020 08:02:58: start model_add_line... INFO @ Fri, 26 Jun 2020 08:02:59: start X-correlation... INFO @ Fri, 26 Jun 2020 08:02:59: end of X-cor INFO @ Fri, 26 Jun 2020 08:02:59: #2 finished! INFO @ Fri, 26 Jun 2020 08:02:59: #2 predicted fragment length is 186 bps INFO @ Fri, 26 Jun 2020 08:02:59: #2 alternative fragment length(s) may be 186 bps INFO @ Fri, 26 Jun 2020 08:02:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.20_model.r WARNING @ Fri, 26 Jun 2020 08:02:59: #2 Since the d (186) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:02:59: #2 You may need to consider one of the other alternative d(s): 186 WARNING @ Fri, 26 Jun 2020 08:02:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:02:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:02:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:03:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:03:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:03:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.10_summits.bed INFO @ Fri, 26 Jun 2020 08:03:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1202 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:03:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:03:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:03:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:03:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2011724/SRX2011724.20_summits.bed INFO @ Fri, 26 Jun 2020 08:03:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (596 records, 4 fields): 14 millis CompletedMACS2peakCalling