Job ID = 14159314 SRX = SRX8976723 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 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: 00:14:23 16190224 reads; of these: 16190224 (100.00%) were paired; of these: 2103722 (12.99%) aligned concordantly 0 times 10395301 (64.21%) aligned concordantly exactly 1 time 3691201 (22.80%) aligned concordantly >1 times ---- 2103722 pairs aligned concordantly 0 times; of these: 1304410 (62.00%) aligned discordantly 1 time ---- 799312 pairs aligned 0 times concordantly or discordantly; of these: 1598624 mates make up the pairs; of these: 258734 (16.18%) aligned 0 times 413929 (25.89%) aligned exactly 1 time 925961 (57.92%) aligned >1 times 99.20% 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] 1029208 / 15374882 = 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 21:14:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976723/SRX8976723.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976723/SRX8976723.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976723/SRX8976723.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 21:14:29: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:14:29: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:14:33: 1000000 INFO @ Wed, 08 Dec 2021 21:14:38: 2000000 INFO @ Wed, 08 Dec 2021 21:14:43: 3000000 INFO @ Wed, 08 Dec 2021 21:14:47: 4000000 INFO @ Wed, 08 Dec 2021 21:14:52: 5000000 INFO @ Wed, 08 Dec 2021 21:14:56: 6000000 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 21:14:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976723/SRX8976723.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976723/SRX8976723.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976723/SRX8976723.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 21:14:59: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:14:59: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:15:01: 7000000 INFO @ Wed, 08 Dec 2021 21:15:04: 1000000 INFO @ Wed, 08 Dec 2021 21:15:06: 8000000 INFO @ Wed, 08 Dec 2021 21:15:10: 2000000 INFO @ Wed, 08 Dec 2021 21:15:12: 9000000 INFO @ Wed, 08 Dec 2021 21:15:15: 3000000 INFO @ Wed, 08 Dec 2021 21:15:17: 10000000 INFO @ Wed, 08 Dec 2021 21:15:20: 4000000 INFO @ Wed, 08 Dec 2021 21:15:22: 11000000 INFO @ Wed, 08 Dec 2021 21:15:25: 5000000 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 21:15:28: 12000000 INFO @ Wed, 08 Dec 2021 21:15:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976723/SRX8976723.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976723/SRX8976723.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976723/SRX8976723.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 21:15:29: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:15:29: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:15:31: 6000000 INFO @ Wed, 08 Dec 2021 21:15:33: 13000000 INFO @ Wed, 08 Dec 2021 21:15:35: 1000000 INFO @ Wed, 08 Dec 2021 21:15:37: 7000000 INFO @ Wed, 08 Dec 2021 21:15:39: 14000000 INFO @ Wed, 08 Dec 2021 21:15:41: 2000000 INFO @ Wed, 08 Dec 2021 21:15:43: 8000000 INFO @ Wed, 08 Dec 2021 21:15:45: 15000000 INFO @ Wed, 08 Dec 2021 21:15:47: 3000000 INFO @ Wed, 08 Dec 2021 21:15:49: 9000000 INFO @ Wed, 08 Dec 2021 21:15:51: 16000000 INFO @ Wed, 08 Dec 2021 21:15:54: 4000000 INFO @ Wed, 08 Dec 2021 21:15:54: 10000000 INFO @ Wed, 08 Dec 2021 21:15:57: 17000000 INFO @ Wed, 08 Dec 2021 21:16:00: 5000000 INFO @ Wed, 08 Dec 2021 21:16:00: 11000000 INFO @ Wed, 08 Dec 2021 21:16:03: 18000000 INFO @ Wed, 08 Dec 2021 21:16:06: 6000000 INFO @ Wed, 08 Dec 2021 21:16:06: 12000000 INFO @ Wed, 08 Dec 2021 21:16:09: 19000000 INFO @ Wed, 08 Dec 2021 21:16:12: 13000000 INFO @ Wed, 08 Dec 2021 21:16:12: 7000000 INFO @ Wed, 08 Dec 2021 21:16:15: 20000000 INFO @ Wed, 08 Dec 2021 21:16:18: 14000000 INFO @ Wed, 08 Dec 2021 21:16:19: 8000000 INFO @ Wed, 08 Dec 2021 21:16:21: 21000000 INFO @ Wed, 08 Dec 2021 21:16:24: 15000000 INFO @ Wed, 08 Dec 2021 21:16:25: 9000000 INFO @ Wed, 08 Dec 2021 21:16:27: 22000000 INFO @ Wed, 08 Dec 2021 21:16:30: 16000000 INFO @ Wed, 08 Dec 2021 21:16:31: 10000000 INFO @ Wed, 08 Dec 2021 21:16:32: 23000000 INFO @ Wed, 08 Dec 2021 21:16:36: 17000000 INFO @ Wed, 08 Dec 2021 21:16:37: 11000000 INFO @ Wed, 08 Dec 2021 21:16:38: 24000000 INFO @ Wed, 08 Dec 2021 21:16:42: 18000000 INFO @ Wed, 08 Dec 2021 21:16:44: 12000000 INFO @ Wed, 08 Dec 2021 21:16:44: 25000000 INFO @ Wed, 08 Dec 2021 21:16:47: 19000000 INFO @ Wed, 08 Dec 2021 21:16:50: 26000000 INFO @ Wed, 08 Dec 2021 21:16:51: 13000000 INFO @ Wed, 08 Dec 2021 21:16:53: 20000000 INFO @ Wed, 08 Dec 2021 21:16:56: 27000000 INFO @ Wed, 08 Dec 2021 21:16:57: 14000000 INFO @ Wed, 08 Dec 2021 21:16:59: 21000000 INFO @ Wed, 08 Dec 2021 21:17:02: 28000000 INFO @ Wed, 08 Dec 2021 21:17:04: 15000000 INFO @ Wed, 08 Dec 2021 21:17:05: 22000000 INFO @ Wed, 08 Dec 2021 21:17:08: 29000000 INFO @ Wed, 08 Dec 2021 21:17:11: 16000000 INFO @ Wed, 08 Dec 2021 21:17:11: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:17:14: 30000000 INFO @ Wed, 08 Dec 2021 21:17:14: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:17:14: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:17:14: #1 total tags in treatment: 13115470 INFO @ Wed, 08 Dec 2021 21:17:14: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:17:14: #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 21:17:14: #1 tags after filtering in treatment: 10577166 INFO @ Wed, 08 Dec 2021 21:17:14: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 08 Dec 2021 21:17:14: #1 finished! INFO @ Wed, 08 Dec 2021 21:17:14: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:17:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:17:15: #2 number of paired peaks: 3006 INFO @ Wed, 08 Dec 2021 21:17:15: start model_add_line... INFO @ Wed, 08 Dec 2021 21:17:15: start X-correlation... INFO @ Wed, 08 Dec 2021 21:17:15: end of X-cor INFO @ Wed, 08 Dec 2021 21:17:15: #2 finished! INFO @ Wed, 08 Dec 2021 21:17:15: #2 predicted fragment length is 231 bps INFO @ Wed, 08 Dec 2021 21:17:15: #2 alternative fragment length(s) may be 2,231,255 bps INFO @ Wed, 08 Dec 2021 21:17:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976723/SRX8976723.05_model.r INFO @ Wed, 08 Dec 2021 21:17:16: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:17:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:17:17: 24000000 INFO @ Wed, 08 Dec 2021 21:17:17: 17000000 INFO @ Wed, 08 Dec 2021 21:17:23: 25000000 INFO @ Wed, 08 Dec 2021 21:17:24: 18000000 INFO @ Wed, 08 Dec 2021 21:17:28: 26000000 INFO @ Wed, 08 Dec 2021 21:17:31: 19000000 INFO @ Wed, 08 Dec 2021 21:17:34: 27000000 INFO @ Wed, 08 Dec 2021 21:17:38: 20000000 INFO @ Wed, 08 Dec 2021 21:17:40: 28000000 INFO @ Wed, 08 Dec 2021 21:17:44: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:17:44: 21000000 INFO @ Wed, 08 Dec 2021 21:17:46: 29000000 INFO @ Wed, 08 Dec 2021 21:17:51: 22000000 INFO @ Wed, 08 Dec 2021 21:17:52: 30000000 INFO @ Wed, 08 Dec 2021 21:17:52: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:17:52: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:17:52: #1 total tags in treatment: 13115470 INFO @ Wed, 08 Dec 2021 21:17:52: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:17:52: #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 21:17:52: #1 tags after filtering in treatment: 10577166 INFO @ Wed, 08 Dec 2021 21:17:52: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 08 Dec 2021 21:17:52: #1 finished! INFO @ Wed, 08 Dec 2021 21:17:52: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:17:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:17:53: #2 number of paired peaks: 3006 INFO @ Wed, 08 Dec 2021 21:17:53: start model_add_line... INFO @ Wed, 08 Dec 2021 21:17:53: start X-correlation... INFO @ Wed, 08 Dec 2021 21:17:53: end of X-cor INFO @ Wed, 08 Dec 2021 21:17:53: #2 finished! INFO @ Wed, 08 Dec 2021 21:17:53: #2 predicted fragment length is 231 bps INFO @ Wed, 08 Dec 2021 21:17:53: #2 alternative fragment length(s) may be 2,231,255 bps INFO @ Wed, 08 Dec 2021 21:17:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976723/SRX8976723.10_model.r INFO @ Wed, 08 Dec 2021 21:17:54: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:17:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:17:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976723/SRX8976723.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:17:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976723/SRX8976723.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:17:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976723/SRX8976723.05_summits.bed BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:17:57: Done! INFO @ Wed, 08 Dec 2021 21:17:57: 23000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1778 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:18:03: 24000000 INFO @ Wed, 08 Dec 2021 21:18:09: 25000000 INFO @ Wed, 08 Dec 2021 21:18:15: 26000000 INFO @ Wed, 08 Dec 2021 21:18:21: 27000000 INFO @ Wed, 08 Dec 2021 21:18:23: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:18:27: 28000000 INFO @ Wed, 08 Dec 2021 21:18:33: 29000000 INFO @ Wed, 08 Dec 2021 21:18:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976723/SRX8976723.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:18:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976723/SRX8976723.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:18:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976723/SRX8976723.10_summits.bed INFO @ Wed, 08 Dec 2021 21:18:34: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (807 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:18:39: 30000000 INFO @ Wed, 08 Dec 2021 21:18:39: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:18:39: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:18:39: #1 total tags in treatment: 13115470 INFO @ Wed, 08 Dec 2021 21:18:39: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:18:39: #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 21:18:39: #1 tags after filtering in treatment: 10577166 INFO @ Wed, 08 Dec 2021 21:18:39: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 08 Dec 2021 21:18:39: #1 finished! INFO @ Wed, 08 Dec 2021 21:18:39: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:18:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:18:40: #2 number of paired peaks: 3006 INFO @ Wed, 08 Dec 2021 21:18:40: start model_add_line... INFO @ Wed, 08 Dec 2021 21:18:40: start X-correlation... INFO @ Wed, 08 Dec 2021 21:18:40: end of X-cor INFO @ Wed, 08 Dec 2021 21:18:40: #2 finished! INFO @ Wed, 08 Dec 2021 21:18:40: #2 predicted fragment length is 231 bps INFO @ Wed, 08 Dec 2021 21:18:40: #2 alternative fragment length(s) may be 2,231,255 bps INFO @ Wed, 08 Dec 2021 21:18:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976723/SRX8976723.20_model.r INFO @ Wed, 08 Dec 2021 21:18:41: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:18:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:19:09: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:19:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976723/SRX8976723.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:19:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976723/SRX8976723.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:19:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976723/SRX8976723.20_summits.bed INFO @ Wed, 08 Dec 2021 21:19:21: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (335 records, 4 fields): 24 millis CompletedMACS2peakCalling