Job ID = 14159416 SRX = SRX8976745 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: 00:25:31 18497933 reads; of these: 18497933 (100.00%) were paired; of these: 2539668 (13.73%) aligned concordantly 0 times 11123671 (60.13%) aligned concordantly exactly 1 time 4834594 (26.14%) aligned concordantly >1 times ---- 2539668 pairs aligned concordantly 0 times; of these: 1480929 (58.31%) aligned discordantly 1 time ---- 1058739 pairs aligned 0 times concordantly or discordantly; of these: 2117478 mates make up the pairs; of these: 332323 (15.69%) aligned 0 times 551788 (26.06%) aligned exactly 1 time 1233367 (58.25%) aligned >1 times 99.10% overall alignment rate Time searching: 00:25:31 Overall time: 00:25:31 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] 1185305 / 17422981 = 0.0680 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 22:09:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.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 22:09:50: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:09:50: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:09:58: 1000000 INFO @ Wed, 08 Dec 2021 22:10:05: 2000000 INFO @ Wed, 08 Dec 2021 22:10:12: 3000000 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 22:10:20: 4000000 INFO @ Wed, 08 Dec 2021 22:10:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.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 22:10:21: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:10:21: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:10:27: 5000000 INFO @ Wed, 08 Dec 2021 22:10:29: 1000000 INFO @ Wed, 08 Dec 2021 22:10:34: 6000000 INFO @ Wed, 08 Dec 2021 22:10:37: 2000000 INFO @ Wed, 08 Dec 2021 22:10:42: 7000000 INFO @ Wed, 08 Dec 2021 22:10:45: 3000000 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 22:10:49: 8000000 INFO @ Wed, 08 Dec 2021 22:10:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.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 22:10:50: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:10:50: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:10:52: 4000000 INFO @ Wed, 08 Dec 2021 22:10:56: 9000000 INFO @ Wed, 08 Dec 2021 22:10:58: 1000000 INFO @ Wed, 08 Dec 2021 22:11:00: 5000000 INFO @ Wed, 08 Dec 2021 22:11:04: 10000000 INFO @ Wed, 08 Dec 2021 22:11:06: 2000000 INFO @ Wed, 08 Dec 2021 22:11:07: 6000000 INFO @ Wed, 08 Dec 2021 22:11:11: 11000000 INFO @ Wed, 08 Dec 2021 22:11:13: 3000000 INFO @ Wed, 08 Dec 2021 22:11:14: 7000000 INFO @ Wed, 08 Dec 2021 22:11:19: 12000000 INFO @ Wed, 08 Dec 2021 22:11:21: 4000000 INFO @ Wed, 08 Dec 2021 22:11:21: 8000000 INFO @ Wed, 08 Dec 2021 22:11:26: 13000000 INFO @ Wed, 08 Dec 2021 22:11:28: 5000000 INFO @ Wed, 08 Dec 2021 22:11:29: 9000000 INFO @ Wed, 08 Dec 2021 22:11:33: 14000000 INFO @ Wed, 08 Dec 2021 22:11:35: 6000000 INFO @ Wed, 08 Dec 2021 22:11:36: 10000000 INFO @ Wed, 08 Dec 2021 22:11:40: 15000000 INFO @ Wed, 08 Dec 2021 22:11:42: 7000000 INFO @ Wed, 08 Dec 2021 22:11:44: 11000000 INFO @ Wed, 08 Dec 2021 22:11:48: 16000000 INFO @ Wed, 08 Dec 2021 22:11:49: 8000000 INFO @ Wed, 08 Dec 2021 22:11:51: 12000000 INFO @ Wed, 08 Dec 2021 22:11:55: 17000000 INFO @ Wed, 08 Dec 2021 22:11:56: 9000000 INFO @ Wed, 08 Dec 2021 22:11:58: 13000000 INFO @ Wed, 08 Dec 2021 22:12:02: 18000000 INFO @ Wed, 08 Dec 2021 22:12:04: 10000000 INFO @ Wed, 08 Dec 2021 22:12:05: 14000000 INFO @ Wed, 08 Dec 2021 22:12:10: 19000000 INFO @ Wed, 08 Dec 2021 22:12:11: 11000000 INFO @ Wed, 08 Dec 2021 22:12:13: 15000000 INFO @ Wed, 08 Dec 2021 22:12:17: 20000000 INFO @ Wed, 08 Dec 2021 22:12:19: 12000000 INFO @ Wed, 08 Dec 2021 22:12:20: 16000000 INFO @ Wed, 08 Dec 2021 22:12:25: 21000000 INFO @ Wed, 08 Dec 2021 22:12:27: 13000000 INFO @ Wed, 08 Dec 2021 22:12:28: 17000000 INFO @ Wed, 08 Dec 2021 22:12:33: 22000000 INFO @ Wed, 08 Dec 2021 22:12:34: 14000000 INFO @ Wed, 08 Dec 2021 22:12:36: 18000000 INFO @ Wed, 08 Dec 2021 22:12:41: 23000000 INFO @ Wed, 08 Dec 2021 22:12:42: 15000000 INFO @ Wed, 08 Dec 2021 22:12:43: 19000000 INFO @ Wed, 08 Dec 2021 22:12:48: 24000000 INFO @ Wed, 08 Dec 2021 22:12:50: 16000000 INFO @ Wed, 08 Dec 2021 22:12:51: 20000000 INFO @ Wed, 08 Dec 2021 22:12:55: 25000000 INFO @ Wed, 08 Dec 2021 22:12:57: 17000000 INFO @ Wed, 08 Dec 2021 22:12:58: 21000000 INFO @ Wed, 08 Dec 2021 22:13:03: 26000000 INFO @ Wed, 08 Dec 2021 22:13:05: 22000000 INFO @ Wed, 08 Dec 2021 22:13:05: 18000000 INFO @ Wed, 08 Dec 2021 22:13:11: 27000000 INFO @ Wed, 08 Dec 2021 22:13:13: 23000000 INFO @ Wed, 08 Dec 2021 22:13:13: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:13:18: 28000000 INFO @ Wed, 08 Dec 2021 22:13:20: 24000000 INFO @ Wed, 08 Dec 2021 22:13:20: 20000000 INFO @ Wed, 08 Dec 2021 22:13:26: 29000000 INFO @ Wed, 08 Dec 2021 22:13:28: 25000000 INFO @ Wed, 08 Dec 2021 22:13:28: 21000000 INFO @ Wed, 08 Dec 2021 22:13:34: 30000000 INFO @ Wed, 08 Dec 2021 22:13:35: 26000000 INFO @ Wed, 08 Dec 2021 22:13:35: 22000000 INFO @ Wed, 08 Dec 2021 22:13:42: 31000000 INFO @ Wed, 08 Dec 2021 22:13:42: 27000000 INFO @ Wed, 08 Dec 2021 22:13:43: 23000000 INFO @ Wed, 08 Dec 2021 22:13:49: 32000000 INFO @ Wed, 08 Dec 2021 22:13:50: 28000000 INFO @ Wed, 08 Dec 2021 22:13:50: 24000000 INFO @ Wed, 08 Dec 2021 22:13:57: 33000000 INFO @ Wed, 08 Dec 2021 22:13:57: 29000000 INFO @ Wed, 08 Dec 2021 22:13:58: 25000000 INFO @ Wed, 08 Dec 2021 22:14:04: 34000000 INFO @ Wed, 08 Dec 2021 22:14:05: 30000000 INFO @ Wed, 08 Dec 2021 22:14:05: 26000000 INFO @ Wed, 08 Dec 2021 22:14:07: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 22:14:07: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 22:14:07: #1 total tags in treatment: 14832009 INFO @ Wed, 08 Dec 2021 22:14:07: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:14:07: #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 22:14:07: #1 tags after filtering in treatment: 11276627 INFO @ Wed, 08 Dec 2021 22:14:07: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 08 Dec 2021 22:14:07: #1 finished! INFO @ Wed, 08 Dec 2021 22:14:07: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:14:07: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:14:08: #2 number of paired peaks: 4521 INFO @ Wed, 08 Dec 2021 22:14:08: start model_add_line... INFO @ Wed, 08 Dec 2021 22:14:08: start X-correlation... INFO @ Wed, 08 Dec 2021 22:14:08: end of X-cor INFO @ Wed, 08 Dec 2021 22:14:08: #2 finished! INFO @ Wed, 08 Dec 2021 22:14:08: #2 predicted fragment length is 238 bps INFO @ Wed, 08 Dec 2021 22:14:08: #2 alternative fragment length(s) may be 1,218,238,254,275 bps INFO @ Wed, 08 Dec 2021 22:14:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.05_model.r INFO @ Wed, 08 Dec 2021 22:14:08: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:14:08: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:14:12: 31000000 INFO @ Wed, 08 Dec 2021 22:14:12: 27000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:14:19: 32000000 INFO @ Wed, 08 Dec 2021 22:14:20: 28000000 INFO @ Wed, 08 Dec 2021 22:14:26: 33000000 INFO @ Wed, 08 Dec 2021 22:14:27: 29000000 INFO @ Wed, 08 Dec 2021 22:14:33: 34000000 INFO @ Wed, 08 Dec 2021 22:14:34: 30000000 INFO @ Wed, 08 Dec 2021 22:14:35: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 22:14:35: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 22:14:35: #1 total tags in treatment: 14832009 INFO @ Wed, 08 Dec 2021 22:14:35: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:14:35: #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 22:14:36: #1 tags after filtering in treatment: 11276627 INFO @ Wed, 08 Dec 2021 22:14:36: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 08 Dec 2021 22:14:36: #1 finished! INFO @ Wed, 08 Dec 2021 22:14:36: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:14:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:14:37: #2 number of paired peaks: 4521 INFO @ Wed, 08 Dec 2021 22:14:37: start model_add_line... INFO @ Wed, 08 Dec 2021 22:14:37: start X-correlation... INFO @ Wed, 08 Dec 2021 22:14:37: end of X-cor INFO @ Wed, 08 Dec 2021 22:14:37: #2 finished! INFO @ Wed, 08 Dec 2021 22:14:37: #2 predicted fragment length is 238 bps INFO @ Wed, 08 Dec 2021 22:14:37: #2 alternative fragment length(s) may be 1,218,238,254,275 bps INFO @ Wed, 08 Dec 2021 22:14:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.10_model.r INFO @ Wed, 08 Dec 2021 22:14:37: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:14:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:14:40: 31000000 INFO @ Wed, 08 Dec 2021 22:14:47: 32000000 INFO @ Wed, 08 Dec 2021 22:14:51: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:14:53: 33000000 INFO @ Wed, 08 Dec 2021 22:15:00: 34000000 INFO @ Wed, 08 Dec 2021 22:15:02: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 22:15:02: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 22:15:02: #1 total tags in treatment: 14832009 INFO @ Wed, 08 Dec 2021 22:15:02: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:15:02: #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 22:15:02: #1 tags after filtering in treatment: 11276627 INFO @ Wed, 08 Dec 2021 22:15:02: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 08 Dec 2021 22:15:02: #1 finished! INFO @ Wed, 08 Dec 2021 22:15:02: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:15:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:15:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:15:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:15:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.05_summits.bed INFO @ Wed, 08 Dec 2021 22:15:03: Done! INFO @ Wed, 08 Dec 2021 22:15:04: #2 number of paired peaks: 4521 INFO @ Wed, 08 Dec 2021 22:15:04: start model_add_line... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2356 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:15:04: start X-correlation... INFO @ Wed, 08 Dec 2021 22:15:04: end of X-cor INFO @ Wed, 08 Dec 2021 22:15:04: #2 finished! INFO @ Wed, 08 Dec 2021 22:15:04: #2 predicted fragment length is 238 bps INFO @ Wed, 08 Dec 2021 22:15:04: #2 alternative fragment length(s) may be 1,218,238,254,275 bps INFO @ Wed, 08 Dec 2021 22:15:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.20_model.r INFO @ Wed, 08 Dec 2021 22:15:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:15:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:15:19: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:15:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:15:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:15:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.10_summits.bed INFO @ Wed, 08 Dec 2021 22:15:31: Done! pass1 - making usageList (7 chroms): 14 millis pass2 - checking and writing primary data (1022 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:15:46: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:15:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:15:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:15:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976745/SRX8976745.20_summits.bed INFO @ Wed, 08 Dec 2021 22:15:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (396 records, 4 fields): 2 millis CompletedMACS2peakCalling