Job ID = 14159062 SRX = SRX8976723 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16190224 spots for SRR12483267/SRR12483267.sra Written 16190224 spots for SRR12483267/SRR12483267.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159314 ("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: 00:14:51 16190224 reads; of these: 16190224 (100.00%) were paired; of these: 2103813 (12.99%) aligned concordantly 0 times 10395338 (64.21%) aligned concordantly exactly 1 time 3691073 (22.80%) aligned concordantly >1 times ---- 2103813 pairs aligned concordantly 0 times; of these: 1304342 (62.00%) aligned discordantly 1 time ---- 799471 pairs aligned 0 times concordantly or discordantly; of these: 1598942 mates make up the pairs; of these: 258993 (16.20%) aligned 0 times 414003 (25.89%) aligned exactly 1 time 925946 (57.91%) aligned >1 times 99.20% overall alignment rate Time searching: 00:14:51 Overall time: 00:14:51 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] 1029200 / 15374750 = 0.0669 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 19:06:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.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 @ Wed, 08 Dec 2021 19:06:40: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:06:40: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:06:46: 1000000 INFO @ Wed, 08 Dec 2021 19:06:52: 2000000 INFO @ Wed, 08 Dec 2021 19:06:58: 3000000 INFO @ Wed, 08 Dec 2021 19:07:03: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 19:07:09: 5000000 INFO @ Wed, 08 Dec 2021 19:07:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.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 @ Wed, 08 Dec 2021 19:07:10: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:07:10: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:07:15: 6000000 INFO @ Wed, 08 Dec 2021 19:07:16: 1000000 INFO @ Wed, 08 Dec 2021 19:07:21: 7000000 INFO @ Wed, 08 Dec 2021 19:07:22: 2000000 INFO @ Wed, 08 Dec 2021 19:07:28: 8000000 INFO @ Wed, 08 Dec 2021 19:07:28: 3000000 INFO @ Wed, 08 Dec 2021 19:07:34: 4000000 INFO @ Wed, 08 Dec 2021 19:07:34: 9000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 19:07:40: 5000000 INFO @ Wed, 08 Dec 2021 19:07:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.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 @ Wed, 08 Dec 2021 19:07:40: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:07:40: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:07:40: 10000000 INFO @ Wed, 08 Dec 2021 19:07:46: 6000000 INFO @ Wed, 08 Dec 2021 19:07:47: 1000000 INFO @ Wed, 08 Dec 2021 19:07:47: 11000000 INFO @ Wed, 08 Dec 2021 19:07:52: 7000000 INFO @ Wed, 08 Dec 2021 19:07:52: 2000000 INFO @ Wed, 08 Dec 2021 19:07:53: 12000000 INFO @ Wed, 08 Dec 2021 19:07:57: 8000000 INFO @ Wed, 08 Dec 2021 19:07:58: 3000000 INFO @ Wed, 08 Dec 2021 19:08:00: 13000000 INFO @ Wed, 08 Dec 2021 19:08:03: 9000000 INFO @ Wed, 08 Dec 2021 19:08:05: 4000000 INFO @ Wed, 08 Dec 2021 19:08:06: 14000000 INFO @ Wed, 08 Dec 2021 19:08:10: 10000000 INFO @ Wed, 08 Dec 2021 19:08:11: 5000000 INFO @ Wed, 08 Dec 2021 19:08:13: 15000000 INFO @ Wed, 08 Dec 2021 19:08:16: 11000000 INFO @ Wed, 08 Dec 2021 19:08:18: 6000000 INFO @ Wed, 08 Dec 2021 19:08:20: 16000000 INFO @ Wed, 08 Dec 2021 19:08:22: 12000000 INFO @ Wed, 08 Dec 2021 19:08:25: 7000000 INFO @ Wed, 08 Dec 2021 19:08:27: 17000000 INFO @ Wed, 08 Dec 2021 19:08:28: 13000000 INFO @ Wed, 08 Dec 2021 19:08:31: 8000000 INFO @ Wed, 08 Dec 2021 19:08:33: 18000000 INFO @ Wed, 08 Dec 2021 19:08:34: 14000000 INFO @ Wed, 08 Dec 2021 19:08:38: 9000000 INFO @ Wed, 08 Dec 2021 19:08:40: 15000000 INFO @ Wed, 08 Dec 2021 19:08:40: 19000000 INFO @ Wed, 08 Dec 2021 19:08:45: 10000000 INFO @ Wed, 08 Dec 2021 19:08:46: 16000000 INFO @ Wed, 08 Dec 2021 19:08:46: 20000000 INFO @ Wed, 08 Dec 2021 19:08:52: 17000000 INFO @ Wed, 08 Dec 2021 19:08:52: 11000000 INFO @ Wed, 08 Dec 2021 19:08:53: 21000000 INFO @ Wed, 08 Dec 2021 19:08:58: 18000000 INFO @ Wed, 08 Dec 2021 19:08:59: 12000000 INFO @ Wed, 08 Dec 2021 19:08:59: 22000000 INFO @ Wed, 08 Dec 2021 19:09:04: 19000000 INFO @ Wed, 08 Dec 2021 19:09:06: 13000000 INFO @ Wed, 08 Dec 2021 19:09:06: 23000000 INFO @ Wed, 08 Dec 2021 19:09:10: 20000000 INFO @ Wed, 08 Dec 2021 19:09:12: 24000000 INFO @ Wed, 08 Dec 2021 19:09:12: 14000000 INFO @ Wed, 08 Dec 2021 19:09:16: 21000000 INFO @ Wed, 08 Dec 2021 19:09:19: 25000000 INFO @ Wed, 08 Dec 2021 19:09:19: 15000000 INFO @ Wed, 08 Dec 2021 19:09:21: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 19:09:25: 26000000 INFO @ Wed, 08 Dec 2021 19:09:26: 16000000 INFO @ Wed, 08 Dec 2021 19:09:27: 23000000 INFO @ Wed, 08 Dec 2021 19:09:31: 27000000 INFO @ Wed, 08 Dec 2021 19:09:33: 17000000 INFO @ Wed, 08 Dec 2021 19:09:33: 24000000 INFO @ Wed, 08 Dec 2021 19:09:37: 28000000 INFO @ Wed, 08 Dec 2021 19:09:39: 25000000 INFO @ Wed, 08 Dec 2021 19:09:40: 18000000 INFO @ Wed, 08 Dec 2021 19:09:44: 29000000 INFO @ Wed, 08 Dec 2021 19:09:45: 26000000 INFO @ Wed, 08 Dec 2021 19:09:47: 19000000 INFO @ Wed, 08 Dec 2021 19:09:50: 30000000 INFO @ Wed, 08 Dec 2021 19:09:51: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:09:51: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:09:51: #1 total tags in treatment: 13115384 INFO @ Wed, 08 Dec 2021 19:09:51: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:09:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 19:09:51: #1 tags after filtering in treatment: 10577076 INFO @ Wed, 08 Dec 2021 19:09:51: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 08 Dec 2021 19:09:51: #1 finished! INFO @ Wed, 08 Dec 2021 19:09:51: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:09:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:09:51: 27000000 INFO @ Wed, 08 Dec 2021 19:09:52: #2 number of paired peaks: 3005 INFO @ Wed, 08 Dec 2021 19:09:52: start model_add_line... INFO @ Wed, 08 Dec 2021 19:09:52: start X-correlation... INFO @ Wed, 08 Dec 2021 19:09:52: end of X-cor INFO @ Wed, 08 Dec 2021 19:09:52: #2 finished! INFO @ Wed, 08 Dec 2021 19:09:52: #2 predicted fragment length is 231 bps INFO @ Wed, 08 Dec 2021 19:09:52: #2 alternative fragment length(s) may be 2,231,254 bps INFO @ Wed, 08 Dec 2021 19:09:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.05_model.r INFO @ Wed, 08 Dec 2021 19:09:52: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:09:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:09:54: 20000000 INFO @ Wed, 08 Dec 2021 19:09:58: 28000000 INFO @ Wed, 08 Dec 2021 19:10:01: 21000000 INFO @ Wed, 08 Dec 2021 19:10:04: 29000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 19:10:07: 22000000 INFO @ Wed, 08 Dec 2021 19:10:10: 30000000 INFO @ Wed, 08 Dec 2021 19:10:10: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:10:10: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:10:10: #1 total tags in treatment: 13115384 INFO @ Wed, 08 Dec 2021 19:10:10: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:10:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 19:10:10: #1 tags after filtering in treatment: 10577076 INFO @ Wed, 08 Dec 2021 19:10:10: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 08 Dec 2021 19:10:10: #1 finished! INFO @ Wed, 08 Dec 2021 19:10:10: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:10:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:10:11: #2 number of paired peaks: 3005 INFO @ Wed, 08 Dec 2021 19:10:11: start model_add_line... INFO @ Wed, 08 Dec 2021 19:10:11: start X-correlation... INFO @ Wed, 08 Dec 2021 19:10:11: end of X-cor INFO @ Wed, 08 Dec 2021 19:10:11: #2 finished! INFO @ Wed, 08 Dec 2021 19:10:11: #2 predicted fragment length is 231 bps INFO @ Wed, 08 Dec 2021 19:10:11: #2 alternative fragment length(s) may be 2,231,254 bps INFO @ Wed, 08 Dec 2021 19:10:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.10_model.r INFO @ Wed, 08 Dec 2021 19:10:11: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:10:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:10:14: 23000000 INFO @ Wed, 08 Dec 2021 19:10:20: 24000000 INFO @ Wed, 08 Dec 2021 19:10:21: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:10:26: 25000000 INFO @ Wed, 08 Dec 2021 19:10:32: 26000000 INFO @ Wed, 08 Dec 2021 19:10:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.05_peaks.xls INFO @ Wed, 08 Dec 2021 19:10:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:10:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.05_summits.bed INFO @ Wed, 08 Dec 2021 19:10:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1776 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:10:38: 27000000 INFO @ Wed, 08 Dec 2021 19:10:39: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:10:43: 28000000 INFO @ Wed, 08 Dec 2021 19:10:49: 29000000 INFO @ Wed, 08 Dec 2021 19:10:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.10_peaks.xls INFO @ Wed, 08 Dec 2021 19:10:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:10:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.10_summits.bed INFO @ Wed, 08 Dec 2021 19:10:50: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (808 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:10:56: 30000000 INFO @ Wed, 08 Dec 2021 19:10:56: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:10:56: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:10:56: #1 total tags in treatment: 13115384 INFO @ Wed, 08 Dec 2021 19:10:56: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:10:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 19:10:56: #1 tags after filtering in treatment: 10577076 INFO @ Wed, 08 Dec 2021 19:10:56: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 08 Dec 2021 19:10:56: #1 finished! INFO @ Wed, 08 Dec 2021 19:10:56: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:10:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:10:57: #2 number of paired peaks: 3005 INFO @ Wed, 08 Dec 2021 19:10:57: start model_add_line... INFO @ Wed, 08 Dec 2021 19:10:57: start X-correlation... INFO @ Wed, 08 Dec 2021 19:10:57: end of X-cor INFO @ Wed, 08 Dec 2021 19:10:57: #2 finished! INFO @ Wed, 08 Dec 2021 19:10:57: #2 predicted fragment length is 231 bps INFO @ Wed, 08 Dec 2021 19:10:57: #2 alternative fragment length(s) may be 2,231,254 bps INFO @ Wed, 08 Dec 2021 19:10:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.20_model.r INFO @ Wed, 08 Dec 2021 19:10:57: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:10:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:11:27: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:11:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.20_peaks.xls INFO @ Wed, 08 Dec 2021 19:11:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:11:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976723/SRX8976723.20_summits.bed INFO @ Wed, 08 Dec 2021 19:11:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (336 records, 4 fields): 1 millis CompletedMACS2peakCalling