Job ID = 14159411 SRX = SRX8976744 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: 00:18:08 19563967 reads; of these: 19563967 (100.00%) were paired; of these: 2187819 (11.18%) aligned concordantly 0 times 12363310 (63.19%) aligned concordantly exactly 1 time 5012838 (25.62%) aligned concordantly >1 times ---- 2187819 pairs aligned concordantly 0 times; of these: 1196979 (54.71%) aligned discordantly 1 time ---- 990840 pairs aligned 0 times concordantly or discordantly; of these: 1981680 mates make up the pairs; of these: 455522 (22.99%) aligned 0 times 486502 (24.55%) aligned exactly 1 time 1039656 (52.46%) aligned >1 times 98.84% overall alignment rate Time searching: 00:18:08 Overall time: 00:18:08 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] 1530044 / 18557220 = 0.0825 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 21:58:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.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 21:58:17: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:58:17: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:58:21: 1000000 INFO @ Wed, 08 Dec 2021 21:58:26: 2000000 INFO @ Wed, 08 Dec 2021 21:58:30: 3000000 INFO @ Wed, 08 Dec 2021 21:58:35: 4000000 INFO @ Wed, 08 Dec 2021 21:58:39: 5000000 INFO @ Wed, 08 Dec 2021 21:58:43: 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 21:58:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.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 21:58:46: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:58:46: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:58:48: 7000000 INFO @ Wed, 08 Dec 2021 21:58:53: 1000000 INFO @ Wed, 08 Dec 2021 21:58:53: 8000000 INFO @ Wed, 08 Dec 2021 21:58:59: 2000000 INFO @ Wed, 08 Dec 2021 21:58:59: 9000000 INFO @ Wed, 08 Dec 2021 21:59:04: 10000000 INFO @ Wed, 08 Dec 2021 21:59:05: 3000000 INFO @ Wed, 08 Dec 2021 21:59:10: 11000000 INFO @ Wed, 08 Dec 2021 21:59:11: 4000000 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 21:59:16: 12000000 INFO @ Wed, 08 Dec 2021 21:59:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.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 21:59:16: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:59:16: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:59:17: 5000000 INFO @ Wed, 08 Dec 2021 21:59:22: 13000000 INFO @ Wed, 08 Dec 2021 21:59:22: 1000000 INFO @ Wed, 08 Dec 2021 21:59:23: 6000000 INFO @ Wed, 08 Dec 2021 21:59:27: 2000000 INFO @ Wed, 08 Dec 2021 21:59:27: 14000000 INFO @ Wed, 08 Dec 2021 21:59:29: 7000000 INFO @ Wed, 08 Dec 2021 21:59:33: 3000000 INFO @ Wed, 08 Dec 2021 21:59:33: 15000000 INFO @ Wed, 08 Dec 2021 21:59:36: 8000000 INFO @ Wed, 08 Dec 2021 21:59:38: 4000000 INFO @ Wed, 08 Dec 2021 21:59:40: 16000000 INFO @ Wed, 08 Dec 2021 21:59:42: 9000000 INFO @ Wed, 08 Dec 2021 21:59:43: 5000000 INFO @ Wed, 08 Dec 2021 21:59:45: 17000000 INFO @ Wed, 08 Dec 2021 21:59:48: 10000000 INFO @ Wed, 08 Dec 2021 21:59:48: 6000000 INFO @ Wed, 08 Dec 2021 21:59:51: 18000000 INFO @ Wed, 08 Dec 2021 21:59:54: 7000000 INFO @ Wed, 08 Dec 2021 21:59:54: 11000000 INFO @ Wed, 08 Dec 2021 21:59:56: 19000000 INFO @ Wed, 08 Dec 2021 21:59:59: 8000000 INFO @ Wed, 08 Dec 2021 22:00:00: 12000000 INFO @ Wed, 08 Dec 2021 22:00:02: 20000000 INFO @ Wed, 08 Dec 2021 22:00:04: 9000000 INFO @ Wed, 08 Dec 2021 22:00:07: 13000000 INFO @ Wed, 08 Dec 2021 22:00:08: 21000000 INFO @ Wed, 08 Dec 2021 22:00:10: 10000000 INFO @ Wed, 08 Dec 2021 22:00:13: 14000000 INFO @ Wed, 08 Dec 2021 22:00:13: 22000000 INFO @ Wed, 08 Dec 2021 22:00:15: 11000000 INFO @ Wed, 08 Dec 2021 22:00:19: 23000000 INFO @ Wed, 08 Dec 2021 22:00:19: 15000000 INFO @ Wed, 08 Dec 2021 22:00:20: 12000000 INFO @ Wed, 08 Dec 2021 22:00:24: 24000000 INFO @ Wed, 08 Dec 2021 22:00:25: 16000000 INFO @ Wed, 08 Dec 2021 22:00:26: 13000000 INFO @ Wed, 08 Dec 2021 22:00:30: 25000000 INFO @ Wed, 08 Dec 2021 22:00:31: 14000000 INFO @ Wed, 08 Dec 2021 22:00:31: 17000000 INFO @ Wed, 08 Dec 2021 22:00:35: 26000000 INFO @ Wed, 08 Dec 2021 22:00:36: 15000000 INFO @ Wed, 08 Dec 2021 22:00:38: 18000000 INFO @ Wed, 08 Dec 2021 22:00:40: 27000000 INFO @ Wed, 08 Dec 2021 22:00:42: 16000000 INFO @ Wed, 08 Dec 2021 22:00:44: 19000000 INFO @ Wed, 08 Dec 2021 22:00:46: 28000000 INFO @ Wed, 08 Dec 2021 22:00:47: 17000000 INFO @ Wed, 08 Dec 2021 22:00:50: 20000000 INFO @ Wed, 08 Dec 2021 22:00:51: 29000000 INFO @ Wed, 08 Dec 2021 22:00:53: 18000000 INFO @ Wed, 08 Dec 2021 22:00:56: 21000000 INFO @ Wed, 08 Dec 2021 22:00:56: 30000000 INFO @ Wed, 08 Dec 2021 22:00:58: 19000000 INFO @ Wed, 08 Dec 2021 22:01:02: 31000000 INFO @ Wed, 08 Dec 2021 22:01:02: 22000000 INFO @ Wed, 08 Dec 2021 22:01:03: 20000000 INFO @ Wed, 08 Dec 2021 22:01:07: 32000000 INFO @ Wed, 08 Dec 2021 22:01:09: 23000000 INFO @ Wed, 08 Dec 2021 22:01:09: 21000000 INFO @ Wed, 08 Dec 2021 22:01:13: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:01:14: 22000000 INFO @ Wed, 08 Dec 2021 22:01:15: 24000000 INFO @ Wed, 08 Dec 2021 22:01:18: 34000000 INFO @ Wed, 08 Dec 2021 22:01:20: 23000000 INFO @ Wed, 08 Dec 2021 22:01:21: 25000000 INFO @ Wed, 08 Dec 2021 22:01:23: 35000000 INFO @ Wed, 08 Dec 2021 22:01:25: 24000000 INFO @ Wed, 08 Dec 2021 22:01:27: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 22:01:27: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 22:01:27: #1 total tags in treatment: 15904091 INFO @ Wed, 08 Dec 2021 22:01:27: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:01:27: #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 22:01:27: #1 tags after filtering in treatment: 12179058 INFO @ Wed, 08 Dec 2021 22:01:27: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 22:01:27: #1 finished! INFO @ Wed, 08 Dec 2021 22:01:27: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:01:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:01:27: 26000000 INFO @ Wed, 08 Dec 2021 22:01:28: #2 number of paired peaks: 4058 INFO @ Wed, 08 Dec 2021 22:01:28: start model_add_line... INFO @ Wed, 08 Dec 2021 22:01:28: start X-correlation... INFO @ Wed, 08 Dec 2021 22:01:28: end of X-cor INFO @ Wed, 08 Dec 2021 22:01:28: #2 finished! INFO @ Wed, 08 Dec 2021 22:01:28: #2 predicted fragment length is 237 bps INFO @ Wed, 08 Dec 2021 22:01:28: #2 alternative fragment length(s) may be 1,237 bps INFO @ Wed, 08 Dec 2021 22:01:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.05_model.r INFO @ Wed, 08 Dec 2021 22:01:28: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:01:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:01:30: 25000000 INFO @ Wed, 08 Dec 2021 22:01:33: 27000000 INFO @ Wed, 08 Dec 2021 22:01:36: 26000000 INFO @ Wed, 08 Dec 2021 22:01:40: 28000000 INFO @ Wed, 08 Dec 2021 22:01:41: 27000000 INFO @ Wed, 08 Dec 2021 22:01:46: 29000000 INFO @ Wed, 08 Dec 2021 22:01:46: 28000000 INFO @ Wed, 08 Dec 2021 22:01:52: 29000000 INFO @ Wed, 08 Dec 2021 22:01:52: 30000000 INFO @ Wed, 08 Dec 2021 22:01:57: 30000000 INFO @ Wed, 08 Dec 2021 22:01:58: 31000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:02:02: 31000000 INFO @ Wed, 08 Dec 2021 22:02:03: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:02:04: 32000000 INFO @ Wed, 08 Dec 2021 22:02:08: 32000000 INFO @ Wed, 08 Dec 2021 22:02:10: 33000000 INFO @ Wed, 08 Dec 2021 22:02:14: 33000000 INFO @ Wed, 08 Dec 2021 22:02:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:02:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:02:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.05_summits.bed INFO @ Wed, 08 Dec 2021 22:02:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2227 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:02:17: 34000000 INFO @ Wed, 08 Dec 2021 22:02:19: 34000000 INFO @ Wed, 08 Dec 2021 22:02:23: 35000000 INFO @ Wed, 08 Dec 2021 22:02:25: 35000000 INFO @ Wed, 08 Dec 2021 22:02:27: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 22:02:27: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 22:02:27: #1 total tags in treatment: 15904091 INFO @ Wed, 08 Dec 2021 22:02:27: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:02:27: #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 22:02:27: #1 tags after filtering in treatment: 12179058 INFO @ Wed, 08 Dec 2021 22:02:27: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 22:02:27: #1 finished! INFO @ Wed, 08 Dec 2021 22:02:27: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:02:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:02:28: #2 number of paired peaks: 4058 INFO @ Wed, 08 Dec 2021 22:02:28: start model_add_line... INFO @ Wed, 08 Dec 2021 22:02:28: start X-correlation... INFO @ Wed, 08 Dec 2021 22:02:28: end of X-cor INFO @ Wed, 08 Dec 2021 22:02:28: #2 finished! INFO @ Wed, 08 Dec 2021 22:02:28: #2 predicted fragment length is 237 bps INFO @ Wed, 08 Dec 2021 22:02:28: #2 alternative fragment length(s) may be 1,237 bps INFO @ Wed, 08 Dec 2021 22:02:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.10_model.r INFO @ Wed, 08 Dec 2021 22:02:28: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:02:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:02:28: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 22:02:28: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 22:02:28: #1 total tags in treatment: 15904091 INFO @ Wed, 08 Dec 2021 22:02:28: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:02:28: #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 22:02:29: #1 tags after filtering in treatment: 12179058 INFO @ Wed, 08 Dec 2021 22:02:29: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 22:02:29: #1 finished! INFO @ Wed, 08 Dec 2021 22:02:29: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:02:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:02:30: #2 number of paired peaks: 4058 INFO @ Wed, 08 Dec 2021 22:02:30: start model_add_line... INFO @ Wed, 08 Dec 2021 22:02:30: start X-correlation... INFO @ Wed, 08 Dec 2021 22:02:30: end of X-cor INFO @ Wed, 08 Dec 2021 22:02:30: #2 finished! INFO @ Wed, 08 Dec 2021 22:02:30: #2 predicted fragment length is 237 bps INFO @ Wed, 08 Dec 2021 22:02:30: #2 alternative fragment length(s) may be 1,237 bps INFO @ Wed, 08 Dec 2021 22:02:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.20_model.r INFO @ Wed, 08 Dec 2021 22:02:30: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:02:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:03:03: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:03:05: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:03:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:03:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:03:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.10_summits.bed INFO @ Wed, 08 Dec 2021 22:03:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (959 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:03:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:03:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:03:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976744/SRX8976744.20_summits.bed INFO @ Wed, 08 Dec 2021 22:03:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (381 records, 4 fields): 6 millis CompletedMACS2peakCalling