Job ID = 14159405 SRX = SRX8976747 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: 00:14:42 15274019 reads; of these: 15274019 (100.00%) were paired; of these: 1848446 (12.10%) aligned concordantly 0 times 10445125 (68.38%) aligned concordantly exactly 1 time 2980448 (19.51%) aligned concordantly >1 times ---- 1848446 pairs aligned concordantly 0 times; of these: 1133221 (61.31%) aligned discordantly 1 time ---- 715225 pairs aligned 0 times concordantly or discordantly; of these: 1430450 mates make up the pairs; of these: 429422 (30.02%) aligned 0 times 340886 (23.83%) aligned exactly 1 time 660142 (46.15%) aligned >1 times 98.59% overall alignment rate Time searching: 00:14:42 Overall time: 00:14:42 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] 1152904 / 14546557 = 0.0793 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 21:52:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.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 21:52:09: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:52:09: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:52:14: 1000000 INFO @ Wed, 08 Dec 2021 21:52:18: 2000000 INFO @ Wed, 08 Dec 2021 21:52:22: 3000000 INFO @ Wed, 08 Dec 2021 21:52:26: 4000000 INFO @ Wed, 08 Dec 2021 21:52:31: 5000000 INFO @ Wed, 08 Dec 2021 21:52:35: 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 21:52:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.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 21:52:39: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:52:39: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:52:39: 7000000 INFO @ Wed, 08 Dec 2021 21:52:43: 1000000 INFO @ Wed, 08 Dec 2021 21:52:43: 8000000 INFO @ Wed, 08 Dec 2021 21:52:47: 9000000 INFO @ Wed, 08 Dec 2021 21:52:47: 2000000 INFO @ Wed, 08 Dec 2021 21:52:51: 10000000 INFO @ Wed, 08 Dec 2021 21:52:52: 3000000 INFO @ Wed, 08 Dec 2021 21:52:55: 11000000 INFO @ Wed, 08 Dec 2021 21:52:56: 4000000 INFO @ Wed, 08 Dec 2021 21:52:59: 12000000 INFO @ Wed, 08 Dec 2021 21:53:00: 5000000 INFO @ Wed, 08 Dec 2021 21:53:03: 13000000 INFO @ Wed, 08 Dec 2021 21:53:05: 6000000 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 21:53:07: 14000000 INFO @ Wed, 08 Dec 2021 21:53:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.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 21:53:09: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:53:09: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:53:09: 7000000 INFO @ Wed, 08 Dec 2021 21:53:11: 15000000 INFO @ Wed, 08 Dec 2021 21:53:13: 1000000 INFO @ Wed, 08 Dec 2021 21:53:14: 8000000 INFO @ Wed, 08 Dec 2021 21:53:16: 16000000 INFO @ Wed, 08 Dec 2021 21:53:17: 2000000 INFO @ Wed, 08 Dec 2021 21:53:18: 9000000 INFO @ Wed, 08 Dec 2021 21:53:20: 17000000 INFO @ Wed, 08 Dec 2021 21:53:21: 3000000 INFO @ Wed, 08 Dec 2021 21:53:23: 10000000 INFO @ Wed, 08 Dec 2021 21:53:25: 4000000 INFO @ Wed, 08 Dec 2021 21:53:25: 18000000 INFO @ Wed, 08 Dec 2021 21:53:27: 11000000 INFO @ Wed, 08 Dec 2021 21:53:29: 5000000 INFO @ Wed, 08 Dec 2021 21:53:30: 19000000 INFO @ Wed, 08 Dec 2021 21:53:32: 12000000 INFO @ Wed, 08 Dec 2021 21:53:33: 6000000 INFO @ Wed, 08 Dec 2021 21:53:35: 20000000 INFO @ Wed, 08 Dec 2021 21:53:36: 13000000 INFO @ Wed, 08 Dec 2021 21:53:37: 7000000 INFO @ Wed, 08 Dec 2021 21:53:39: 21000000 INFO @ Wed, 08 Dec 2021 21:53:41: 14000000 INFO @ Wed, 08 Dec 2021 21:53:41: 8000000 INFO @ Wed, 08 Dec 2021 21:53:43: 22000000 INFO @ Wed, 08 Dec 2021 21:53:45: 9000000 INFO @ Wed, 08 Dec 2021 21:53:45: 15000000 INFO @ Wed, 08 Dec 2021 21:53:47: 23000000 INFO @ Wed, 08 Dec 2021 21:53:49: 10000000 INFO @ Wed, 08 Dec 2021 21:53:49: 16000000 INFO @ Wed, 08 Dec 2021 21:53:52: 24000000 INFO @ Wed, 08 Dec 2021 21:53:53: 11000000 INFO @ Wed, 08 Dec 2021 21:53:54: 17000000 INFO @ Wed, 08 Dec 2021 21:53:56: 25000000 INFO @ Wed, 08 Dec 2021 21:53:57: 12000000 INFO @ Wed, 08 Dec 2021 21:53:58: 18000000 INFO @ Wed, 08 Dec 2021 21:54:00: 26000000 INFO @ Wed, 08 Dec 2021 21:54:01: 13000000 INFO @ Wed, 08 Dec 2021 21:54:03: 19000000 INFO @ Wed, 08 Dec 2021 21:54:05: 27000000 INFO @ Wed, 08 Dec 2021 21:54:06: 14000000 INFO @ Wed, 08 Dec 2021 21:54:07: 20000000 INFO @ Wed, 08 Dec 2021 21:54:08: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:54:08: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:54:08: #1 total tags in treatment: 12337750 INFO @ Wed, 08 Dec 2021 21:54:08: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:54:08: #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 21:54:08: #1 tags after filtering in treatment: 10591385 INFO @ Wed, 08 Dec 2021 21:54:08: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 08 Dec 2021 21:54:08: #1 finished! INFO @ Wed, 08 Dec 2021 21:54:08: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:54:08: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:54:09: #2 number of paired peaks: 1400 INFO @ Wed, 08 Dec 2021 21:54:09: start model_add_line... INFO @ Wed, 08 Dec 2021 21:54:09: start X-correlation... INFO @ Wed, 08 Dec 2021 21:54:09: end of X-cor INFO @ Wed, 08 Dec 2021 21:54:09: #2 finished! INFO @ Wed, 08 Dec 2021 21:54:09: #2 predicted fragment length is 184 bps INFO @ Wed, 08 Dec 2021 21:54:09: #2 alternative fragment length(s) may be 2,153,165,184,196,198 bps INFO @ Wed, 08 Dec 2021 21:54:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.05_model.r INFO @ Wed, 08 Dec 2021 21:54:09: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:54:09: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:54:10: 15000000 INFO @ Wed, 08 Dec 2021 21:54:12: 21000000 INFO @ Wed, 08 Dec 2021 21:54:14: 16000000 INFO @ Wed, 08 Dec 2021 21:54:16: 22000000 INFO @ Wed, 08 Dec 2021 21:54:18: 17000000 INFO @ Wed, 08 Dec 2021 21:54:20: 23000000 INFO @ Wed, 08 Dec 2021 21:54:22: 18000000 INFO @ Wed, 08 Dec 2021 21:54:24: 24000000 INFO @ Wed, 08 Dec 2021 21:54:25: 19000000 INFO @ Wed, 08 Dec 2021 21:54:29: 25000000 INFO @ Wed, 08 Dec 2021 21:54:29: 20000000 INFO @ Wed, 08 Dec 2021 21:54:33: 21000000 INFO @ Wed, 08 Dec 2021 21:54:33: 26000000 INFO @ Wed, 08 Dec 2021 21:54:35: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:54:37: 22000000 INFO @ Wed, 08 Dec 2021 21:54:38: 27000000 INFO @ Wed, 08 Dec 2021 21:54:41: 23000000 INFO @ Wed, 08 Dec 2021 21:54:42: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:54:42: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:54:42: #1 total tags in treatment: 12337750 INFO @ Wed, 08 Dec 2021 21:54:42: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:54:42: #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 21:54:42: #1 tags after filtering in treatment: 10591385 INFO @ Wed, 08 Dec 2021 21:54:42: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 08 Dec 2021 21:54:42: #1 finished! INFO @ Wed, 08 Dec 2021 21:54:42: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:54:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:54:43: #2 number of paired peaks: 1400 INFO @ Wed, 08 Dec 2021 21:54:43: start model_add_line... INFO @ Wed, 08 Dec 2021 21:54:43: start X-correlation... INFO @ Wed, 08 Dec 2021 21:54:43: end of X-cor INFO @ Wed, 08 Dec 2021 21:54:43: #2 finished! INFO @ Wed, 08 Dec 2021 21:54:43: #2 predicted fragment length is 184 bps INFO @ Wed, 08 Dec 2021 21:54:43: #2 alternative fragment length(s) may be 2,153,165,184,196,198 bps INFO @ Wed, 08 Dec 2021 21:54:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.10_model.r INFO @ Wed, 08 Dec 2021 21:54:43: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:54:43: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:54:45: 24000000 INFO @ Wed, 08 Dec 2021 21:54:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:54:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:54:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.05_summits.bed INFO @ Wed, 08 Dec 2021 21:54:47: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (826 records, 4 fields): 135 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:54:49: 25000000 INFO @ Wed, 08 Dec 2021 21:54:53: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:54:57: 27000000 INFO @ Wed, 08 Dec 2021 21:55:00: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:55:00: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:55:00: #1 total tags in treatment: 12337750 INFO @ Wed, 08 Dec 2021 21:55:00: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:55:00: #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 21:55:00: #1 tags after filtering in treatment: 10591385 INFO @ Wed, 08 Dec 2021 21:55:00: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 08 Dec 2021 21:55:00: #1 finished! INFO @ Wed, 08 Dec 2021 21:55:00: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:55:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:55:01: #2 number of paired peaks: 1400 INFO @ Wed, 08 Dec 2021 21:55:01: start model_add_line... INFO @ Wed, 08 Dec 2021 21:55:01: start X-correlation... INFO @ Wed, 08 Dec 2021 21:55:01: end of X-cor INFO @ Wed, 08 Dec 2021 21:55:01: #2 finished! INFO @ Wed, 08 Dec 2021 21:55:01: #2 predicted fragment length is 184 bps INFO @ Wed, 08 Dec 2021 21:55:01: #2 alternative fragment length(s) may be 2,153,165,184,196,198 bps INFO @ Wed, 08 Dec 2021 21:55:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.20_model.r INFO @ Wed, 08 Dec 2021 21:55:01: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:55:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:55:08: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:55:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:55:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:55:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.10_summits.bed INFO @ Wed, 08 Dec 2021 21:55:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (371 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:55:25: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:55:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:55:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:55:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976747/SRX8976747.20_summits.bed INFO @ Wed, 08 Dec 2021 21:55:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (195 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。