Job ID = 6497349 SRX = SRX1995047 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T21:31:35 prefetch.2.10.7: 1) Downloading 'SRR3993979'... 2020-06-25T21:31:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:34:17 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:34:17 prefetch.2.10.7: 1) 'SRR3993979' was downloaded successfully Read 18591839 spots for SRR3993979/SRR3993979.sra Written 18591839 spots for SRR3993979/SRR3993979.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: 00:27:16 18591839 reads; of these: 18591839 (100.00%) were paired; of these: 1311640 (7.05%) aligned concordantly 0 times 11888661 (63.95%) aligned concordantly exactly 1 time 5391538 (29.00%) aligned concordantly >1 times ---- 1311640 pairs aligned concordantly 0 times; of these: 472016 (35.99%) aligned discordantly 1 time ---- 839624 pairs aligned 0 times concordantly or discordantly; of these: 1679248 mates make up the pairs; of these: 1112462 (66.25%) aligned 0 times 265490 (15.81%) aligned exactly 1 time 301296 (17.94%) aligned >1 times 97.01% overall alignment rate Time searching: 00:27:16 Overall time: 00:27:16 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 16 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] 3628198 / 17735532 = 0.2046 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 07:15:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.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 07:15:57: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:15:57: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:16:03: 1000000 INFO @ Fri, 26 Jun 2020 07:16:10: 2000000 INFO @ Fri, 26 Jun 2020 07:16:17: 3000000 INFO @ Fri, 26 Jun 2020 07:16:25: 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 07:16:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.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 07:16:27: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:16:27: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:16:32: 5000000 INFO @ Fri, 26 Jun 2020 07:16:34: 1000000 INFO @ Fri, 26 Jun 2020 07:16:39: 6000000 INFO @ Fri, 26 Jun 2020 07:16:41: 2000000 INFO @ Fri, 26 Jun 2020 07:16:46: 7000000 INFO @ Fri, 26 Jun 2020 07:16:48: 3000000 INFO @ Fri, 26 Jun 2020 07:16:54: 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 @ Fri, 26 Jun 2020 07:16:55: 4000000 INFO @ Fri, 26 Jun 2020 07:16:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.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 07:16:57: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:16:57: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:17:01: 9000000 INFO @ Fri, 26 Jun 2020 07:17:02: 5000000 INFO @ Fri, 26 Jun 2020 07:17:04: 1000000 INFO @ Fri, 26 Jun 2020 07:17:09: 10000000 INFO @ Fri, 26 Jun 2020 07:17:09: 6000000 INFO @ Fri, 26 Jun 2020 07:17:11: 2000000 INFO @ Fri, 26 Jun 2020 07:17:16: 7000000 INFO @ Fri, 26 Jun 2020 07:17:17: 11000000 INFO @ Fri, 26 Jun 2020 07:17:18: 3000000 INFO @ Fri, 26 Jun 2020 07:17:23: 8000000 INFO @ Fri, 26 Jun 2020 07:17:24: 12000000 INFO @ Fri, 26 Jun 2020 07:17:25: 4000000 INFO @ Fri, 26 Jun 2020 07:17:30: 9000000 INFO @ Fri, 26 Jun 2020 07:17:32: 5000000 INFO @ Fri, 26 Jun 2020 07:17:32: 13000000 INFO @ Fri, 26 Jun 2020 07:17:37: 10000000 INFO @ Fri, 26 Jun 2020 07:17:39: 6000000 INFO @ Fri, 26 Jun 2020 07:17:39: 14000000 INFO @ Fri, 26 Jun 2020 07:17:44: 11000000 INFO @ Fri, 26 Jun 2020 07:17:46: 7000000 INFO @ Fri, 26 Jun 2020 07:17:47: 15000000 INFO @ Fri, 26 Jun 2020 07:17:51: 12000000 INFO @ Fri, 26 Jun 2020 07:17:52: 8000000 INFO @ Fri, 26 Jun 2020 07:17:54: 16000000 INFO @ Fri, 26 Jun 2020 07:17:57: 13000000 INFO @ Fri, 26 Jun 2020 07:17:59: 9000000 INFO @ Fri, 26 Jun 2020 07:18:02: 17000000 INFO @ Fri, 26 Jun 2020 07:18:04: 14000000 INFO @ Fri, 26 Jun 2020 07:18:06: 10000000 INFO @ Fri, 26 Jun 2020 07:18:09: 18000000 INFO @ Fri, 26 Jun 2020 07:18:11: 15000000 INFO @ Fri, 26 Jun 2020 07:18:13: 11000000 INFO @ Fri, 26 Jun 2020 07:18:17: 19000000 INFO @ Fri, 26 Jun 2020 07:18:18: 16000000 INFO @ Fri, 26 Jun 2020 07:18:20: 12000000 INFO @ Fri, 26 Jun 2020 07:18:24: 20000000 INFO @ Fri, 26 Jun 2020 07:18:25: 17000000 INFO @ Fri, 26 Jun 2020 07:18:27: 13000000 INFO @ Fri, 26 Jun 2020 07:18:32: 21000000 INFO @ Fri, 26 Jun 2020 07:18:32: 18000000 INFO @ Fri, 26 Jun 2020 07:18:34: 14000000 INFO @ Fri, 26 Jun 2020 07:18:39: 22000000 INFO @ Fri, 26 Jun 2020 07:18:39: 19000000 INFO @ Fri, 26 Jun 2020 07:18:41: 15000000 INFO @ Fri, 26 Jun 2020 07:18:46: 23000000 INFO @ Fri, 26 Jun 2020 07:18:46: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:18:48: 16000000 INFO @ Fri, 26 Jun 2020 07:18:53: 21000000 INFO @ Fri, 26 Jun 2020 07:18:53: 24000000 INFO @ Fri, 26 Jun 2020 07:18:55: 17000000 INFO @ Fri, 26 Jun 2020 07:19:00: 22000000 INFO @ Fri, 26 Jun 2020 07:19:01: 25000000 INFO @ Fri, 26 Jun 2020 07:19:02: 18000000 INFO @ Fri, 26 Jun 2020 07:19:07: 23000000 INFO @ Fri, 26 Jun 2020 07:19:09: 26000000 INFO @ Fri, 26 Jun 2020 07:19:09: 19000000 INFO @ Fri, 26 Jun 2020 07:19:15: 24000000 INFO @ Fri, 26 Jun 2020 07:19:16: 20000000 INFO @ Fri, 26 Jun 2020 07:19:16: 27000000 INFO @ Fri, 26 Jun 2020 07:19:22: 25000000 INFO @ Fri, 26 Jun 2020 07:19:23: 21000000 INFO @ Fri, 26 Jun 2020 07:19:24: 28000000 INFO @ Fri, 26 Jun 2020 07:19:29: 26000000 INFO @ Fri, 26 Jun 2020 07:19:30: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:19:30: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:19:30: #1 total tags in treatment: 13692144 INFO @ Fri, 26 Jun 2020 07:19:30: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:19:30: #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 07:19:30: 22000000 INFO @ Fri, 26 Jun 2020 07:19:30: #1 tags after filtering in treatment: 10772749 INFO @ Fri, 26 Jun 2020 07:19:30: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 26 Jun 2020 07:19:30: #1 finished! INFO @ Fri, 26 Jun 2020 07:19:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:19:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:19:31: #2 number of paired peaks: 1986 INFO @ Fri, 26 Jun 2020 07:19:31: start model_add_line... INFO @ Fri, 26 Jun 2020 07:19:31: start X-correlation... INFO @ Fri, 26 Jun 2020 07:19:31: end of X-cor INFO @ Fri, 26 Jun 2020 07:19:31: #2 finished! INFO @ Fri, 26 Jun 2020 07:19:31: #2 predicted fragment length is 185 bps INFO @ Fri, 26 Jun 2020 07:19:31: #2 alternative fragment length(s) may be 185 bps INFO @ Fri, 26 Jun 2020 07:19:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.05_model.r INFO @ Fri, 26 Jun 2020 07:19:31: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:19:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:19:36: 27000000 INFO @ Fri, 26 Jun 2020 07:19:37: 23000000 INFO @ Fri, 26 Jun 2020 07:19:43: 28000000 INFO @ Fri, 26 Jun 2020 07:19:44: 24000000 INFO @ Fri, 26 Jun 2020 07:19:48: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:19:48: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:19:48: #1 total tags in treatment: 13692144 INFO @ Fri, 26 Jun 2020 07:19:48: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:19:48: #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 07:19:48: #1 tags after filtering in treatment: 10772749 INFO @ Fri, 26 Jun 2020 07:19:48: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 26 Jun 2020 07:19:48: #1 finished! INFO @ Fri, 26 Jun 2020 07:19:48: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:19:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:19:49: #2 number of paired peaks: 1986 INFO @ Fri, 26 Jun 2020 07:19:49: start model_add_line... INFO @ Fri, 26 Jun 2020 07:19:49: start X-correlation... INFO @ Fri, 26 Jun 2020 07:19:49: end of X-cor INFO @ Fri, 26 Jun 2020 07:19:49: #2 finished! INFO @ Fri, 26 Jun 2020 07:19:49: #2 predicted fragment length is 185 bps INFO @ Fri, 26 Jun 2020 07:19:49: #2 alternative fragment length(s) may be 185 bps INFO @ Fri, 26 Jun 2020 07:19:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.10_model.r INFO @ Fri, 26 Jun 2020 07:19:49: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:19:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:19:50: 25000000 INFO @ Fri, 26 Jun 2020 07:19:56: 26000000 INFO @ Fri, 26 Jun 2020 07:20:00: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:20:02: 27000000 INFO @ Fri, 26 Jun 2020 07:20:08: 28000000 INFO @ Fri, 26 Jun 2020 07:20:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:20:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:20:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.05_summits.bed INFO @ Fri, 26 Jun 2020 07:20:13: Done! INFO @ Fri, 26 Jun 2020 07:20:13: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:20:13: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:20:13: #1 total tags in treatment: 13692144 INFO @ Fri, 26 Jun 2020 07:20:13: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:20:13: #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 07:20:13: #1 tags after filtering in treatment: 10772749 INFO @ Fri, 26 Jun 2020 07:20:13: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 26 Jun 2020 07:20:13: #1 finished! INFO @ Fri, 26 Jun 2020 07:20:13: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:20:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:20:14: #2 number of paired peaks: 1986 INFO @ Fri, 26 Jun 2020 07:20:14: start model_add_line... INFO @ Fri, 26 Jun 2020 07:20:14: start X-correlation... INFO @ Fri, 26 Jun 2020 07:20:14: end of X-cor INFO @ Fri, 26 Jun 2020 07:20:14: #2 finished! INFO @ Fri, 26 Jun 2020 07:20:14: #2 predicted fragment length is 185 bps INFO @ Fri, 26 Jun 2020 07:20:14: #2 alternative fragment length(s) may be 185 bps INFO @ Fri, 26 Jun 2020 07:20:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.20_model.r INFO @ Fri, 26 Jun 2020 07:20:14: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:20:14: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4310 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:20:19: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:20:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:20:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:20:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.10_summits.bed INFO @ Fri, 26 Jun 2020 07:20:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2816 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:20:43: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:20:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:20:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:20:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1995047/SRX1995047.20_summits.bed INFO @ Fri, 26 Jun 2020 07:20:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1511 records, 4 fields): 6 millis CompletedMACS2peakCalling