Job ID = 14159419 SRX = SRX8976743 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: 00:17:27 18070562 reads; of these: 18070562 (100.00%) were paired; of these: 2132035 (11.80%) aligned concordantly 0 times 11334284 (62.72%) aligned concordantly exactly 1 time 4604243 (25.48%) aligned concordantly >1 times ---- 2132035 pairs aligned concordantly 0 times; of these: 1197429 (56.16%) aligned discordantly 1 time ---- 934606 pairs aligned 0 times concordantly or discordantly; of these: 1869212 mates make up the pairs; of these: 382138 (20.44%) aligned 0 times 454513 (24.32%) aligned exactly 1 time 1032561 (55.24%) aligned >1 times 98.94% overall alignment rate Time searching: 00:17:27 Overall time: 00:17:27 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] 1319363 / 17120570 = 0.0771 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 22:00:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.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 22:00:31: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:00:31: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:00:35: 1000000 INFO @ Wed, 08 Dec 2021 22:00:40: 2000000 INFO @ Wed, 08 Dec 2021 22:00:44: 3000000 INFO @ Wed, 08 Dec 2021 22:00:49: 4000000 INFO @ Wed, 08 Dec 2021 22:00:53: 5000000 INFO @ Wed, 08 Dec 2021 22:00:58: 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 22:01:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.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 22:01:01: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:01:01: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:01:02: 7000000 INFO @ Wed, 08 Dec 2021 22:01:05: 1000000 INFO @ Wed, 08 Dec 2021 22:01:07: 8000000 INFO @ Wed, 08 Dec 2021 22:01:09: 2000000 INFO @ Wed, 08 Dec 2021 22:01:12: 9000000 INFO @ Wed, 08 Dec 2021 22:01:14: 3000000 INFO @ Wed, 08 Dec 2021 22:01:16: 10000000 INFO @ Wed, 08 Dec 2021 22:01:18: 4000000 INFO @ Wed, 08 Dec 2021 22:01:21: 11000000 INFO @ Wed, 08 Dec 2021 22:01:22: 5000000 INFO @ Wed, 08 Dec 2021 22:01:26: 6000000 INFO @ Wed, 08 Dec 2021 22:01:26: 12000000 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 22:01:30: 7000000 INFO @ Wed, 08 Dec 2021 22:01:30: 13000000 INFO @ Wed, 08 Dec 2021 22:01:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.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 22:01:31: #1 read tag files... INFO @ Wed, 08 Dec 2021 22:01:31: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 22:01:34: 8000000 INFO @ Wed, 08 Dec 2021 22:01:35: 14000000 INFO @ Wed, 08 Dec 2021 22:01:35: 1000000 INFO @ Wed, 08 Dec 2021 22:01:38: 9000000 INFO @ Wed, 08 Dec 2021 22:01:40: 15000000 INFO @ Wed, 08 Dec 2021 22:01:40: 2000000 INFO @ Wed, 08 Dec 2021 22:01:42: 10000000 INFO @ Wed, 08 Dec 2021 22:01:44: 16000000 INFO @ Wed, 08 Dec 2021 22:01:45: 3000000 INFO @ Wed, 08 Dec 2021 22:01:46: 11000000 INFO @ Wed, 08 Dec 2021 22:01:49: 17000000 INFO @ Wed, 08 Dec 2021 22:01:50: 4000000 INFO @ Wed, 08 Dec 2021 22:01:50: 12000000 INFO @ Wed, 08 Dec 2021 22:01:54: 18000000 INFO @ Wed, 08 Dec 2021 22:01:54: 13000000 INFO @ Wed, 08 Dec 2021 22:01:55: 5000000 INFO @ Wed, 08 Dec 2021 22:01:58: 19000000 INFO @ Wed, 08 Dec 2021 22:01:59: 14000000 INFO @ Wed, 08 Dec 2021 22:01:59: 6000000 INFO @ Wed, 08 Dec 2021 22:02:03: 15000000 INFO @ Wed, 08 Dec 2021 22:02:03: 20000000 INFO @ Wed, 08 Dec 2021 22:02:04: 7000000 INFO @ Wed, 08 Dec 2021 22:02:07: 16000000 INFO @ Wed, 08 Dec 2021 22:02:08: 21000000 INFO @ Wed, 08 Dec 2021 22:02:09: 8000000 INFO @ Wed, 08 Dec 2021 22:02:11: 17000000 INFO @ Wed, 08 Dec 2021 22:02:13: 22000000 INFO @ Wed, 08 Dec 2021 22:02:13: 9000000 INFO @ Wed, 08 Dec 2021 22:02:15: 18000000 INFO @ Wed, 08 Dec 2021 22:02:17: 23000000 INFO @ Wed, 08 Dec 2021 22:02:18: 10000000 INFO @ Wed, 08 Dec 2021 22:02:20: 19000000 INFO @ Wed, 08 Dec 2021 22:02:22: 24000000 INFO @ Wed, 08 Dec 2021 22:02:23: 11000000 INFO @ Wed, 08 Dec 2021 22:02:24: 20000000 INFO @ Wed, 08 Dec 2021 22:02:27: 25000000 INFO @ Wed, 08 Dec 2021 22:02:28: 21000000 INFO @ Wed, 08 Dec 2021 22:02:28: 12000000 INFO @ Wed, 08 Dec 2021 22:02:31: 26000000 INFO @ Wed, 08 Dec 2021 22:02:32: 22000000 INFO @ Wed, 08 Dec 2021 22:02:33: 13000000 INFO @ Wed, 08 Dec 2021 22:02:36: 27000000 INFO @ Wed, 08 Dec 2021 22:02:36: 23000000 INFO @ Wed, 08 Dec 2021 22:02:38: 14000000 INFO @ Wed, 08 Dec 2021 22:02:40: 28000000 INFO @ Wed, 08 Dec 2021 22:02:41: 24000000 INFO @ Wed, 08 Dec 2021 22:02:43: 15000000 INFO @ Wed, 08 Dec 2021 22:02:45: 25000000 INFO @ Wed, 08 Dec 2021 22:02:45: 29000000 INFO @ Wed, 08 Dec 2021 22:02:48: 16000000 INFO @ Wed, 08 Dec 2021 22:02:49: 26000000 INFO @ Wed, 08 Dec 2021 22:02:50: 30000000 INFO @ Wed, 08 Dec 2021 22:02:53: 17000000 INFO @ Wed, 08 Dec 2021 22:02:53: 27000000 INFO @ Wed, 08 Dec 2021 22:02:54: 31000000 INFO @ Wed, 08 Dec 2021 22:02:57: 28000000 INFO @ Wed, 08 Dec 2021 22:02:58: 18000000 INFO @ Wed, 08 Dec 2021 22:02:59: 32000000 INFO @ Wed, 08 Dec 2021 22:03:02: 29000000 INFO @ Wed, 08 Dec 2021 22:03:03: 19000000 INFO @ Wed, 08 Dec 2021 22:03:04: 33000000 INFO @ Wed, 08 Dec 2021 22:03:04: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 22:03:04: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 22:03:04: #1 total tags in treatment: 14675738 INFO @ Wed, 08 Dec 2021 22:03:04: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:03:04: #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 22:03:05: #1 tags after filtering in treatment: 11332753 INFO @ Wed, 08 Dec 2021 22:03:05: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 22:03:05: #1 finished! INFO @ Wed, 08 Dec 2021 22:03:05: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:03:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:03:06: #2 number of paired peaks: 4095 INFO @ Wed, 08 Dec 2021 22:03:06: start model_add_line... INFO @ Wed, 08 Dec 2021 22:03:06: start X-correlation... INFO @ Wed, 08 Dec 2021 22:03:06: end of X-cor INFO @ Wed, 08 Dec 2021 22:03:06: #2 finished! INFO @ Wed, 08 Dec 2021 22:03:06: #2 predicted fragment length is 242 bps INFO @ Wed, 08 Dec 2021 22:03:06: #2 alternative fragment length(s) may be 1,230,242,261 bps INFO @ Wed, 08 Dec 2021 22:03:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.05_model.r INFO @ Wed, 08 Dec 2021 22:03:06: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:03:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:03:06: 30000000 INFO @ Wed, 08 Dec 2021 22:03:08: 20000000 INFO @ Wed, 08 Dec 2021 22:03:11: 31000000 INFO @ Wed, 08 Dec 2021 22:03:13: 21000000 INFO @ Wed, 08 Dec 2021 22:03:15: 32000000 INFO @ Wed, 08 Dec 2021 22:03:18: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 22:03:19: 33000000 INFO @ Wed, 08 Dec 2021 22:03:20: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 22:03:20: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 22:03:20: #1 total tags in treatment: 14675738 INFO @ Wed, 08 Dec 2021 22:03:20: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:03:20: #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 22:03:20: #1 tags after filtering in treatment: 11332753 INFO @ Wed, 08 Dec 2021 22:03:20: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 22:03:20: #1 finished! INFO @ Wed, 08 Dec 2021 22:03:20: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:03:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:03:21: #2 number of paired peaks: 4095 INFO @ Wed, 08 Dec 2021 22:03:21: start model_add_line... INFO @ Wed, 08 Dec 2021 22:03:21: start X-correlation... INFO @ Wed, 08 Dec 2021 22:03:21: end of X-cor INFO @ Wed, 08 Dec 2021 22:03:21: #2 finished! INFO @ Wed, 08 Dec 2021 22:03:21: #2 predicted fragment length is 242 bps INFO @ Wed, 08 Dec 2021 22:03:21: #2 alternative fragment length(s) may be 1,230,242,261 bps INFO @ Wed, 08 Dec 2021 22:03:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.10_model.r INFO @ Wed, 08 Dec 2021 22:03:21: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:03:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:03:22: 23000000 INFO @ Wed, 08 Dec 2021 22:03:27: 24000000 INFO @ Wed, 08 Dec 2021 22:03:32: 25000000 INFO @ Wed, 08 Dec 2021 22:03:37: 26000000 INFO @ Wed, 08 Dec 2021 22:03:38: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:03:41: 27000000 INFO @ Wed, 08 Dec 2021 22:03:46: 28000000 INFO @ Wed, 08 Dec 2021 22:03:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.05_peaks.xls INFO @ Wed, 08 Dec 2021 22:03:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:03:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.05_summits.bed INFO @ Wed, 08 Dec 2021 22:03:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2105 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:03:51: 29000000 INFO @ Wed, 08 Dec 2021 22:03:54: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:03:55: 30000000 INFO @ Wed, 08 Dec 2021 22:04:00: 31000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 22:04:05: 32000000 INFO @ Wed, 08 Dec 2021 22:04:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.10_peaks.xls INFO @ Wed, 08 Dec 2021 22:04:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:04:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.10_summits.bed INFO @ Wed, 08 Dec 2021 22:04:06: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (930 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 22:04:10: 33000000 INFO @ Wed, 08 Dec 2021 22:04:11: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 22:04:11: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 22:04:11: #1 total tags in treatment: 14675738 INFO @ Wed, 08 Dec 2021 22:04:11: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 22:04:11: #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 22:04:11: #1 tags after filtering in treatment: 11332753 INFO @ Wed, 08 Dec 2021 22:04:11: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 22:04:11: #1 finished! INFO @ Wed, 08 Dec 2021 22:04:11: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 22:04:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 22:04:12: #2 number of paired peaks: 4095 INFO @ Wed, 08 Dec 2021 22:04:12: start model_add_line... INFO @ Wed, 08 Dec 2021 22:04:12: start X-correlation... INFO @ Wed, 08 Dec 2021 22:04:12: end of X-cor INFO @ Wed, 08 Dec 2021 22:04:12: #2 finished! INFO @ Wed, 08 Dec 2021 22:04:12: #2 predicted fragment length is 242 bps INFO @ Wed, 08 Dec 2021 22:04:12: #2 alternative fragment length(s) may be 1,230,242,261 bps INFO @ Wed, 08 Dec 2021 22:04:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.20_model.r INFO @ Wed, 08 Dec 2021 22:04:12: #3 Call peaks... INFO @ Wed, 08 Dec 2021 22:04:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 22:04:45: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 22:04:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.20_peaks.xls INFO @ Wed, 08 Dec 2021 22:04:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 22:04:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976743/SRX8976743.20_summits.bed INFO @ Wed, 08 Dec 2021 22:04:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (367 records, 4 fields): 1 millis CompletedMACS2peakCalling