Job ID = 14159638 SRX = SRX8976695 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: 00:16:26 15280097 reads; of these: 15280097 (100.00%) were paired; of these: 1084242 (7.10%) aligned concordantly 0 times 11808901 (77.28%) aligned concordantly exactly 1 time 2386954 (15.62%) aligned concordantly >1 times ---- 1084242 pairs aligned concordantly 0 times; of these: 595213 (54.90%) aligned discordantly 1 time ---- 489029 pairs aligned 0 times concordantly or discordantly; of these: 978058 mates make up the pairs; of these: 597544 (61.09%) aligned 0 times 138059 (14.12%) aligned exactly 1 time 242455 (24.79%) aligned >1 times 98.04% overall alignment rate Time searching: 00:16:26 Overall time: 00:16:26 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] 1710185 / 14781828 = 0.1157 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 @ Thu, 09 Dec 2021 00:07:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.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 @ Thu, 09 Dec 2021 00:07:57: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:07:57: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:08:04: 1000000 INFO @ Thu, 09 Dec 2021 00:08:10: 2000000 INFO @ Thu, 09 Dec 2021 00:08:17: 3000000 INFO @ Thu, 09 Dec 2021 00:08:24: 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 @ Thu, 09 Dec 2021 00:08:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.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 @ Thu, 09 Dec 2021 00:08:27: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:08:27: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:08:31: 5000000 INFO @ Thu, 09 Dec 2021 00:08:36: 1000000 INFO @ Thu, 09 Dec 2021 00:08:39: 6000000 INFO @ Thu, 09 Dec 2021 00:08:46: 7000000 INFO @ Thu, 09 Dec 2021 00:08:46: 2000000 INFO @ Thu, 09 Dec 2021 00:08:52: 8000000 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 @ Thu, 09 Dec 2021 00:08:55: 3000000 INFO @ Thu, 09 Dec 2021 00:08:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.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 @ Thu, 09 Dec 2021 00:08:57: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:08:57: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:08:59: 9000000 INFO @ Thu, 09 Dec 2021 00:09:05: 4000000 INFO @ Thu, 09 Dec 2021 00:09:05: 1000000 INFO @ Thu, 09 Dec 2021 00:09:05: 10000000 INFO @ Thu, 09 Dec 2021 00:09:12: 11000000 INFO @ Thu, 09 Dec 2021 00:09:13: 2000000 INFO @ Thu, 09 Dec 2021 00:09:14: 5000000 INFO @ Thu, 09 Dec 2021 00:09:20: 12000000 INFO @ Thu, 09 Dec 2021 00:09:21: 3000000 INFO @ Thu, 09 Dec 2021 00:09:24: 6000000 INFO @ Thu, 09 Dec 2021 00:09:27: 13000000 INFO @ Thu, 09 Dec 2021 00:09:29: 4000000 INFO @ Thu, 09 Dec 2021 00:09:34: 7000000 INFO @ Thu, 09 Dec 2021 00:09:34: 14000000 INFO @ Thu, 09 Dec 2021 00:09:37: 5000000 INFO @ Thu, 09 Dec 2021 00:09:41: 15000000 INFO @ Thu, 09 Dec 2021 00:09:43: 8000000 INFO @ Thu, 09 Dec 2021 00:09:44: 6000000 INFO @ Thu, 09 Dec 2021 00:09:48: 16000000 INFO @ Thu, 09 Dec 2021 00:09:52: 7000000 INFO @ Thu, 09 Dec 2021 00:09:53: 9000000 INFO @ Thu, 09 Dec 2021 00:09:54: 17000000 INFO @ Thu, 09 Dec 2021 00:10:00: 8000000 INFO @ Thu, 09 Dec 2021 00:10:01: 18000000 INFO @ Thu, 09 Dec 2021 00:10:02: 10000000 INFO @ Thu, 09 Dec 2021 00:10:08: 9000000 INFO @ Thu, 09 Dec 2021 00:10:08: 19000000 INFO @ Thu, 09 Dec 2021 00:10:12: 11000000 INFO @ Thu, 09 Dec 2021 00:10:14: 20000000 INFO @ Thu, 09 Dec 2021 00:10:15: 10000000 INFO @ Thu, 09 Dec 2021 00:10:21: 21000000 INFO @ Thu, 09 Dec 2021 00:10:21: 12000000 INFO @ Thu, 09 Dec 2021 00:10:23: 11000000 INFO @ Thu, 09 Dec 2021 00:10:28: 22000000 INFO @ Thu, 09 Dec 2021 00:10:30: 12000000 INFO @ Thu, 09 Dec 2021 00:10:31: 13000000 INFO @ Thu, 09 Dec 2021 00:10:34: 23000000 INFO @ Thu, 09 Dec 2021 00:10:38: 13000000 INFO @ Thu, 09 Dec 2021 00:10:40: 14000000 INFO @ Thu, 09 Dec 2021 00:10:40: 24000000 INFO @ Thu, 09 Dec 2021 00:10:45: 14000000 INFO @ Thu, 09 Dec 2021 00:10:47: 25000000 INFO @ Thu, 09 Dec 2021 00:10:49: 15000000 INFO @ Thu, 09 Dec 2021 00:10:53: 15000000 INFO @ Thu, 09 Dec 2021 00:10:54: 26000000 INFO @ Thu, 09 Dec 2021 00:10:57: #1 tag size is determined as 42 bps INFO @ Thu, 09 Dec 2021 00:10:57: #1 tag size = 42 INFO @ Thu, 09 Dec 2021 00:10:57: #1 total tags in treatment: 12532613 INFO @ Thu, 09 Dec 2021 00:10:57: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:10:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:10:58: #1 tags after filtering in treatment: 11314528 INFO @ Thu, 09 Dec 2021 00:10:58: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 00:10:58: #1 finished! INFO @ Thu, 09 Dec 2021 00:10:58: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:10:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:10:59: #2 number of paired peaks: 1254 INFO @ Thu, 09 Dec 2021 00:10:59: start model_add_line... INFO @ Thu, 09 Dec 2021 00:10:59: start X-correlation... INFO @ Thu, 09 Dec 2021 00:10:59: end of X-cor INFO @ Thu, 09 Dec 2021 00:10:59: #2 finished! INFO @ Thu, 09 Dec 2021 00:10:59: #2 predicted fragment length is 203 bps INFO @ Thu, 09 Dec 2021 00:10:59: #2 alternative fragment length(s) may be 2,169,203 bps INFO @ Thu, 09 Dec 2021 00:10:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.05_model.r INFO @ Thu, 09 Dec 2021 00:10:59: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:10:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:10:59: 16000000 INFO @ Thu, 09 Dec 2021 00:11:00: 16000000 INFO @ Thu, 09 Dec 2021 00:11:08: 17000000 INFO @ Thu, 09 Dec 2021 00:11:08: 17000000 INFO @ Thu, 09 Dec 2021 00:11:16: 18000000 INFO @ Thu, 09 Dec 2021 00:11:17: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:11:23: 19000000 INFO @ Thu, 09 Dec 2021 00:11:27: 19000000 INFO @ Thu, 09 Dec 2021 00:11:30: 20000000 INFO @ Thu, 09 Dec 2021 00:11:36: 20000000 INFO @ Thu, 09 Dec 2021 00:11:36: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:11:38: 21000000 INFO @ Thu, 09 Dec 2021 00:11:44: 21000000 INFO @ Thu, 09 Dec 2021 00:11:45: 22000000 INFO @ Thu, 09 Dec 2021 00:11:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:11:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:11:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.05_summits.bed INFO @ Thu, 09 Dec 2021 00:11:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1071 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:11:53: 23000000 INFO @ Thu, 09 Dec 2021 00:11:53: 22000000 INFO @ Thu, 09 Dec 2021 00:12:00: 24000000 INFO @ Thu, 09 Dec 2021 00:12:02: 23000000 INFO @ Thu, 09 Dec 2021 00:12:07: 25000000 INFO @ Thu, 09 Dec 2021 00:12:11: 24000000 INFO @ Thu, 09 Dec 2021 00:12:14: 26000000 INFO @ Thu, 09 Dec 2021 00:12:18: #1 tag size is determined as 42 bps INFO @ Thu, 09 Dec 2021 00:12:18: #1 tag size = 42 INFO @ Thu, 09 Dec 2021 00:12:18: #1 total tags in treatment: 12532613 INFO @ Thu, 09 Dec 2021 00:12:18: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:12:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:12:19: #1 tags after filtering in treatment: 11314528 INFO @ Thu, 09 Dec 2021 00:12:19: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 00:12:19: #1 finished! INFO @ Thu, 09 Dec 2021 00:12:19: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:12:19: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:12:19: 25000000 INFO @ Thu, 09 Dec 2021 00:12:20: #2 number of paired peaks: 1254 INFO @ Thu, 09 Dec 2021 00:12:20: start model_add_line... INFO @ Thu, 09 Dec 2021 00:12:20: start X-correlation... INFO @ Thu, 09 Dec 2021 00:12:20: end of X-cor INFO @ Thu, 09 Dec 2021 00:12:20: #2 finished! INFO @ Thu, 09 Dec 2021 00:12:20: #2 predicted fragment length is 203 bps INFO @ Thu, 09 Dec 2021 00:12:20: #2 alternative fragment length(s) may be 2,169,203 bps INFO @ Thu, 09 Dec 2021 00:12:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.20_model.r INFO @ Thu, 09 Dec 2021 00:12:20: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:12:20: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:12:28: 26000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:12:32: #1 tag size is determined as 42 bps INFO @ Thu, 09 Dec 2021 00:12:32: #1 tag size = 42 INFO @ Thu, 09 Dec 2021 00:12:32: #1 total tags in treatment: 12532613 INFO @ Thu, 09 Dec 2021 00:12:32: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:12:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:12:33: #1 tags after filtering in treatment: 11314528 INFO @ Thu, 09 Dec 2021 00:12:33: #1 Redundant rate of treatment: 0.10 INFO @ Thu, 09 Dec 2021 00:12:33: #1 finished! INFO @ Thu, 09 Dec 2021 00:12:33: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:12:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:12:34: #2 number of paired peaks: 1254 INFO @ Thu, 09 Dec 2021 00:12:34: start model_add_line... INFO @ Thu, 09 Dec 2021 00:12:34: start X-correlation... INFO @ Thu, 09 Dec 2021 00:12:34: end of X-cor INFO @ Thu, 09 Dec 2021 00:12:34: #2 finished! INFO @ Thu, 09 Dec 2021 00:12:34: #2 predicted fragment length is 203 bps INFO @ Thu, 09 Dec 2021 00:12:34: #2 alternative fragment length(s) may be 2,169,203 bps INFO @ Thu, 09 Dec 2021 00:12:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.10_model.r INFO @ Thu, 09 Dec 2021 00:12:34: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:12:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:12:58: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:13:11: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:13:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:13:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:13:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.20_summits.bed INFO @ Thu, 09 Dec 2021 00:13:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (195 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:13:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:13:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:13:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976695/SRX8976695.10_summits.bed INFO @ Thu, 09 Dec 2021 00:13:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (477 records, 4 fields): 3 millis CompletedMACS2peakCalling