Job ID = 14159632 SRX = SRX8976690 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: 00:15:02 15674404 reads; of these: 15674404 (100.00%) were paired; of these: 1848175 (11.79%) aligned concordantly 0 times 10116694 (64.54%) aligned concordantly exactly 1 time 3709535 (23.67%) aligned concordantly >1 times ---- 1848175 pairs aligned concordantly 0 times; of these: 1054344 (57.05%) aligned discordantly 1 time ---- 793831 pairs aligned 0 times concordantly or discordantly; of these: 1587662 mates make up the pairs; of these: 472112 (29.74%) aligned 0 times 374773 (23.61%) aligned exactly 1 time 740777 (46.66%) aligned >1 times 98.49% overall alignment rate Time searching: 00:15:02 Overall time: 00:15:02 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] 1235607 / 14869885 = 0.0831 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 23:57:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.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 23:57:40: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:57:40: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:57:44: 1000000 INFO @ Wed, 08 Dec 2021 23:57:48: 2000000 INFO @ Wed, 08 Dec 2021 23:57:52: 3000000 INFO @ Wed, 08 Dec 2021 23:57:56: 4000000 INFO @ Wed, 08 Dec 2021 23:58:00: 5000000 INFO @ Wed, 08 Dec 2021 23:58:04: 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 23:58:08: 7000000 INFO @ Wed, 08 Dec 2021 23:58:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.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 23:58:10: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:58:10: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:58:13: 8000000 INFO @ Wed, 08 Dec 2021 23:58:14: 1000000 INFO @ Wed, 08 Dec 2021 23:58:17: 9000000 INFO @ Wed, 08 Dec 2021 23:58:18: 2000000 INFO @ Wed, 08 Dec 2021 23:58:21: 10000000 INFO @ Wed, 08 Dec 2021 23:58:23: 3000000 INFO @ Wed, 08 Dec 2021 23:58:26: 11000000 INFO @ Wed, 08 Dec 2021 23:58:27: 4000000 INFO @ Wed, 08 Dec 2021 23:58:30: 12000000 INFO @ Wed, 08 Dec 2021 23:58:31: 5000000 INFO @ Wed, 08 Dec 2021 23:58:34: 13000000 INFO @ Wed, 08 Dec 2021 23:58:35: 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 23:58:39: 14000000 INFO @ Wed, 08 Dec 2021 23:58:40: 7000000 INFO @ Wed, 08 Dec 2021 23:58:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.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 23:58:40: #1 read tag files... INFO @ Wed, 08 Dec 2021 23:58:40: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 23:58:43: 15000000 INFO @ Wed, 08 Dec 2021 23:58:44: 8000000 INFO @ Wed, 08 Dec 2021 23:58:45: 1000000 INFO @ Wed, 08 Dec 2021 23:58:48: 16000000 INFO @ Wed, 08 Dec 2021 23:58:49: 9000000 INFO @ Wed, 08 Dec 2021 23:58:50: 2000000 INFO @ Wed, 08 Dec 2021 23:58:52: 17000000 INFO @ Wed, 08 Dec 2021 23:58:53: 10000000 INFO @ Wed, 08 Dec 2021 23:58:55: 3000000 INFO @ Wed, 08 Dec 2021 23:58:56: 18000000 INFO @ Wed, 08 Dec 2021 23:58:57: 11000000 INFO @ Wed, 08 Dec 2021 23:59:00: 4000000 INFO @ Wed, 08 Dec 2021 23:59:01: 19000000 INFO @ Wed, 08 Dec 2021 23:59:02: 12000000 INFO @ Wed, 08 Dec 2021 23:59:05: 5000000 INFO @ Wed, 08 Dec 2021 23:59:05: 20000000 INFO @ Wed, 08 Dec 2021 23:59:06: 13000000 INFO @ Wed, 08 Dec 2021 23:59:10: 6000000 INFO @ Wed, 08 Dec 2021 23:59:10: 21000000 INFO @ Wed, 08 Dec 2021 23:59:11: 14000000 INFO @ Wed, 08 Dec 2021 23:59:14: 22000000 INFO @ Wed, 08 Dec 2021 23:59:15: 7000000 INFO @ Wed, 08 Dec 2021 23:59:15: 15000000 INFO @ Wed, 08 Dec 2021 23:59:19: 23000000 INFO @ Wed, 08 Dec 2021 23:59:20: 8000000 INFO @ Wed, 08 Dec 2021 23:59:20: 16000000 INFO @ Wed, 08 Dec 2021 23:59:23: 24000000 INFO @ Wed, 08 Dec 2021 23:59:24: 17000000 INFO @ Wed, 08 Dec 2021 23:59:25: 9000000 INFO @ Wed, 08 Dec 2021 23:59:28: 25000000 INFO @ Wed, 08 Dec 2021 23:59:29: 18000000 INFO @ Wed, 08 Dec 2021 23:59:30: 10000000 INFO @ Wed, 08 Dec 2021 23:59:32: 26000000 INFO @ Wed, 08 Dec 2021 23:59:33: 19000000 INFO @ Wed, 08 Dec 2021 23:59:35: 11000000 INFO @ Wed, 08 Dec 2021 23:59:37: 27000000 INFO @ Wed, 08 Dec 2021 23:59:38: 20000000 INFO @ Wed, 08 Dec 2021 23:59:40: 12000000 INFO @ Wed, 08 Dec 2021 23:59:41: 28000000 INFO @ Wed, 08 Dec 2021 23:59:42: 21000000 INFO @ Wed, 08 Dec 2021 23:59:43: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 23:59:43: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 23:59:43: #1 total tags in treatment: 12647831 INFO @ Wed, 08 Dec 2021 23:59:43: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 23:59:43: #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 23:59:43: #1 tags after filtering in treatment: 10206249 INFO @ Wed, 08 Dec 2021 23:59:43: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 08 Dec 2021 23:59:43: #1 finished! INFO @ Wed, 08 Dec 2021 23:59:43: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 23:59:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 23:59:44: #2 number of paired peaks: 3803 INFO @ Wed, 08 Dec 2021 23:59:44: start model_add_line... INFO @ Wed, 08 Dec 2021 23:59:44: start X-correlation... INFO @ Wed, 08 Dec 2021 23:59:44: end of X-cor INFO @ Wed, 08 Dec 2021 23:59:44: #2 finished! INFO @ Wed, 08 Dec 2021 23:59:44: #2 predicted fragment length is 244 bps INFO @ Wed, 08 Dec 2021 23:59:44: #2 alternative fragment length(s) may be 1,218,244,272 bps INFO @ Wed, 08 Dec 2021 23:59:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.05_model.r INFO @ Wed, 08 Dec 2021 23:59:44: #3 Call peaks... INFO @ Wed, 08 Dec 2021 23:59:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 23:59:45: 13000000 INFO @ Wed, 08 Dec 2021 23:59:46: 22000000 INFO @ Wed, 08 Dec 2021 23:59:50: 14000000 INFO @ Wed, 08 Dec 2021 23:59:51: 23000000 INFO @ Wed, 08 Dec 2021 23:59:55: 15000000 INFO @ Wed, 08 Dec 2021 23:59:56: 24000000 INFO @ Thu, 09 Dec 2021 00:00:00: 16000000 INFO @ Thu, 09 Dec 2021 00:00:00: 25000000 INFO @ Thu, 09 Dec 2021 00:00:04: 26000000 INFO @ Thu, 09 Dec 2021 00:00:05: 17000000 INFO @ Thu, 09 Dec 2021 00:00:09: 27000000 INFO @ Thu, 09 Dec 2021 00:00:10: 18000000 INFO @ Thu, 09 Dec 2021 00:00:14: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:00:14: 28000000 INFO @ Thu, 09 Dec 2021 00:00:15: 19000000 INFO @ Thu, 09 Dec 2021 00:00:16: #1 tag size is determined as 42 bps INFO @ Thu, 09 Dec 2021 00:00:16: #1 tag size = 42 INFO @ Thu, 09 Dec 2021 00:00:16: #1 total tags in treatment: 12647831 INFO @ Thu, 09 Dec 2021 00:00:16: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:00:16: #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 00:00:16: #1 tags after filtering in treatment: 10206249 INFO @ Thu, 09 Dec 2021 00:00:16: #1 Redundant rate of treatment: 0.19 INFO @ Thu, 09 Dec 2021 00:00:16: #1 finished! INFO @ Thu, 09 Dec 2021 00:00:16: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:00:16: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:00:17: #2 number of paired peaks: 3803 INFO @ Thu, 09 Dec 2021 00:00:17: start model_add_line... INFO @ Thu, 09 Dec 2021 00:00:17: start X-correlation... INFO @ Thu, 09 Dec 2021 00:00:17: end of X-cor INFO @ Thu, 09 Dec 2021 00:00:17: #2 finished! INFO @ Thu, 09 Dec 2021 00:00:17: #2 predicted fragment length is 244 bps INFO @ Thu, 09 Dec 2021 00:00:17: #2 alternative fragment length(s) may be 1,218,244,272 bps INFO @ Thu, 09 Dec 2021 00:00:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.10_model.r INFO @ Thu, 09 Dec 2021 00:00:17: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:00:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:00:20: 20000000 INFO @ Thu, 09 Dec 2021 00:00:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:00:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:00:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.05_summits.bed INFO @ Thu, 09 Dec 2021 00:00:24: Done! INFO @ Thu, 09 Dec 2021 00:00:24: 21000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1726 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:00:29: 22000000 INFO @ Thu, 09 Dec 2021 00:00:34: 23000000 INFO @ Thu, 09 Dec 2021 00:00:39: 24000000 INFO @ Thu, 09 Dec 2021 00:00:44: 25000000 INFO @ Thu, 09 Dec 2021 00:00:46: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:00:48: 26000000 INFO @ Thu, 09 Dec 2021 00:00:53: 27000000 INFO @ Thu, 09 Dec 2021 00:00:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:00:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:00:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.10_summits.bed INFO @ Thu, 09 Dec 2021 00:00:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (717 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:00:58: 28000000 INFO @ Thu, 09 Dec 2021 00:01:00: #1 tag size is determined as 42 bps INFO @ Thu, 09 Dec 2021 00:01:00: #1 tag size = 42 INFO @ Thu, 09 Dec 2021 00:01:00: #1 total tags in treatment: 12647831 INFO @ Thu, 09 Dec 2021 00:01:00: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:01:00: #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 00:01:00: #1 tags after filtering in treatment: 10206249 INFO @ Thu, 09 Dec 2021 00:01:00: #1 Redundant rate of treatment: 0.19 INFO @ Thu, 09 Dec 2021 00:01:00: #1 finished! INFO @ Thu, 09 Dec 2021 00:01:00: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:01:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:01:01: #2 number of paired peaks: 3803 INFO @ Thu, 09 Dec 2021 00:01:01: start model_add_line... INFO @ Thu, 09 Dec 2021 00:01:01: start X-correlation... INFO @ Thu, 09 Dec 2021 00:01:01: end of X-cor INFO @ Thu, 09 Dec 2021 00:01:01: #2 finished! INFO @ Thu, 09 Dec 2021 00:01:01: #2 predicted fragment length is 244 bps INFO @ Thu, 09 Dec 2021 00:01:01: #2 alternative fragment length(s) may be 1,218,244,272 bps INFO @ Thu, 09 Dec 2021 00:01:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.20_model.r INFO @ Thu, 09 Dec 2021 00:01:01: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:01:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:01:31: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:01:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:01:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:01:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976690/SRX8976690.20_summits.bed INFO @ Thu, 09 Dec 2021 00:01:42: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (299 records, 4 fields): 2 millis CompletedMACS2peakCalling