Job ID = 14159357 SRX = SRX8976739 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: 00:12:46 15492033 reads; of these: 15492033 (100.00%) were paired; of these: 1326286 (8.56%) aligned concordantly 0 times 12308796 (79.45%) aligned concordantly exactly 1 time 1856951 (11.99%) aligned concordantly >1 times ---- 1326286 pairs aligned concordantly 0 times; of these: 992255 (74.81%) aligned discordantly 1 time ---- 334031 pairs aligned 0 times concordantly or discordantly; of these: 668062 mates make up the pairs; of these: 185602 (27.78%) aligned 0 times 212305 (31.78%) aligned exactly 1 time 270155 (40.44%) aligned >1 times 99.40% overall alignment rate Time searching: 00:12:46 Overall time: 00:12:46 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] 473020 / 15123873 = 0.0313 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 21:30:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.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 21:30:21: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:30:21: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:30:26: 1000000 INFO @ Wed, 08 Dec 2021 21:30:31: 2000000 INFO @ Wed, 08 Dec 2021 21:30:35: 3000000 INFO @ Wed, 08 Dec 2021 21:30:40: 4000000 INFO @ Wed, 08 Dec 2021 21:30:44: 5000000 INFO @ Wed, 08 Dec 2021 21:30:49: 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 21:30:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.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 21:30:51: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:30:51: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:30:53: 7000000 INFO @ Wed, 08 Dec 2021 21:30:56: 1000000 INFO @ Wed, 08 Dec 2021 21:30:58: 8000000 INFO @ Wed, 08 Dec 2021 21:31:00: 2000000 INFO @ Wed, 08 Dec 2021 21:31:02: 9000000 INFO @ Wed, 08 Dec 2021 21:31:05: 3000000 INFO @ Wed, 08 Dec 2021 21:31:06: 10000000 INFO @ Wed, 08 Dec 2021 21:31:09: 4000000 INFO @ Wed, 08 Dec 2021 21:31:11: 11000000 INFO @ Wed, 08 Dec 2021 21:31:13: 5000000 INFO @ Wed, 08 Dec 2021 21:31:15: 12000000 INFO @ Wed, 08 Dec 2021 21:31:18: 6000000 INFO @ Wed, 08 Dec 2021 21:31:19: 13000000 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 21:31:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.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 21:31:21: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:31:21: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:31:22: 7000000 INFO @ Wed, 08 Dec 2021 21:31:24: 14000000 INFO @ Wed, 08 Dec 2021 21:31:27: 1000000 INFO @ Wed, 08 Dec 2021 21:31:27: 8000000 INFO @ Wed, 08 Dec 2021 21:31:29: 15000000 INFO @ Wed, 08 Dec 2021 21:31:32: 2000000 INFO @ Wed, 08 Dec 2021 21:31:32: 9000000 INFO @ Wed, 08 Dec 2021 21:31:34: 16000000 INFO @ Wed, 08 Dec 2021 21:31:37: 10000000 INFO @ Wed, 08 Dec 2021 21:31:37: 3000000 INFO @ Wed, 08 Dec 2021 21:31:39: 17000000 INFO @ Wed, 08 Dec 2021 21:31:42: 11000000 INFO @ Wed, 08 Dec 2021 21:31:43: 4000000 INFO @ Wed, 08 Dec 2021 21:31:44: 18000000 INFO @ Wed, 08 Dec 2021 21:31:47: 12000000 INFO @ Wed, 08 Dec 2021 21:31:48: 5000000 INFO @ Wed, 08 Dec 2021 21:31:49: 19000000 INFO @ Wed, 08 Dec 2021 21:31:52: 13000000 INFO @ Wed, 08 Dec 2021 21:31:53: 6000000 INFO @ Wed, 08 Dec 2021 21:31:54: 20000000 INFO @ Wed, 08 Dec 2021 21:31:57: 14000000 INFO @ Wed, 08 Dec 2021 21:31:59: 7000000 INFO @ Wed, 08 Dec 2021 21:31:59: 21000000 INFO @ Wed, 08 Dec 2021 21:32:02: 15000000 INFO @ Wed, 08 Dec 2021 21:32:04: 22000000 INFO @ Wed, 08 Dec 2021 21:32:04: 8000000 INFO @ Wed, 08 Dec 2021 21:32:07: 16000000 INFO @ Wed, 08 Dec 2021 21:32:09: 23000000 INFO @ Wed, 08 Dec 2021 21:32:09: 9000000 INFO @ Wed, 08 Dec 2021 21:32:12: 17000000 INFO @ Wed, 08 Dec 2021 21:32:14: 24000000 INFO @ Wed, 08 Dec 2021 21:32:15: 10000000 INFO @ Wed, 08 Dec 2021 21:32:17: 18000000 INFO @ Wed, 08 Dec 2021 21:32:19: 25000000 INFO @ Wed, 08 Dec 2021 21:32:21: 11000000 INFO @ Wed, 08 Dec 2021 21:32:22: 19000000 INFO @ Wed, 08 Dec 2021 21:32:24: 26000000 INFO @ Wed, 08 Dec 2021 21:32:26: 12000000 INFO @ Wed, 08 Dec 2021 21:32:27: 20000000 INFO @ Wed, 08 Dec 2021 21:32:29: 27000000 INFO @ Wed, 08 Dec 2021 21:32:32: 21000000 INFO @ Wed, 08 Dec 2021 21:32:32: 13000000 INFO @ Wed, 08 Dec 2021 21:32:34: 28000000 INFO @ Wed, 08 Dec 2021 21:32:37: 22000000 INFO @ Wed, 08 Dec 2021 21:32:38: 14000000 INFO @ Wed, 08 Dec 2021 21:32:39: 29000000 INFO @ Wed, 08 Dec 2021 21:32:42: 23000000 INFO @ Wed, 08 Dec 2021 21:32:43: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:32:43: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:32:43: #1 total tags in treatment: 13715961 INFO @ Wed, 08 Dec 2021 21:32:43: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:32:43: #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 21:32:43: #1 tags after filtering in treatment: 12701982 INFO @ Wed, 08 Dec 2021 21:32:43: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:32:43: #1 finished! INFO @ Wed, 08 Dec 2021 21:32:43: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:32:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:32:43: 15000000 INFO @ Wed, 08 Dec 2021 21:32:44: #2 number of paired peaks: 332 WARNING @ Wed, 08 Dec 2021 21:32:44: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Wed, 08 Dec 2021 21:32:44: start model_add_line... INFO @ Wed, 08 Dec 2021 21:32:44: start X-correlation... INFO @ Wed, 08 Dec 2021 21:32:44: end of X-cor INFO @ Wed, 08 Dec 2021 21:32:44: #2 finished! INFO @ Wed, 08 Dec 2021 21:32:44: #2 predicted fragment length is 132 bps INFO @ Wed, 08 Dec 2021 21:32:44: #2 alternative fragment length(s) may be 3,132,150,173,176 bps INFO @ Wed, 08 Dec 2021 21:32:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.05_model.r INFO @ Wed, 08 Dec 2021 21:32:44: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:32:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:32:47: 24000000 INFO @ Wed, 08 Dec 2021 21:32:49: 16000000 INFO @ Wed, 08 Dec 2021 21:32:52: 25000000 INFO @ Wed, 08 Dec 2021 21:32:55: 17000000 INFO @ Wed, 08 Dec 2021 21:32:56: 26000000 INFO @ Wed, 08 Dec 2021 21:33:00: 18000000 INFO @ Wed, 08 Dec 2021 21:33:01: 27000000 INFO @ Wed, 08 Dec 2021 21:33:06: 28000000 INFO @ Wed, 08 Dec 2021 21:33:06: 19000000 INFO @ Wed, 08 Dec 2021 21:33:08: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:33:11: 29000000 INFO @ Wed, 08 Dec 2021 21:33:12: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:33:15: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:33:15: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:33:15: #1 total tags in treatment: 13715961 INFO @ Wed, 08 Dec 2021 21:33:15: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:33:15: #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 21:33:15: #1 tags after filtering in treatment: 12701982 INFO @ Wed, 08 Dec 2021 21:33:15: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:33:15: #1 finished! INFO @ Wed, 08 Dec 2021 21:33:15: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:33:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:33:16: #2 number of paired peaks: 332 WARNING @ Wed, 08 Dec 2021 21:33:16: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Wed, 08 Dec 2021 21:33:16: start model_add_line... INFO @ Wed, 08 Dec 2021 21:33:16: start X-correlation... INFO @ Wed, 08 Dec 2021 21:33:16: end of X-cor INFO @ Wed, 08 Dec 2021 21:33:16: #2 finished! INFO @ Wed, 08 Dec 2021 21:33:16: #2 predicted fragment length is 132 bps INFO @ Wed, 08 Dec 2021 21:33:16: #2 alternative fragment length(s) may be 3,132,150,173,176 bps INFO @ Wed, 08 Dec 2021 21:33:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.10_model.r INFO @ Wed, 08 Dec 2021 21:33:17: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:33:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:33:17: 21000000 INFO @ Wed, 08 Dec 2021 21:33:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:33:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:33:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.05_summits.bed INFO @ Wed, 08 Dec 2021 21:33:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (369 records, 4 fields): 51 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:33:22: 22000000 INFO @ Wed, 08 Dec 2021 21:33:28: 23000000 INFO @ Wed, 08 Dec 2021 21:33:33: 24000000 INFO @ Wed, 08 Dec 2021 21:33:38: 25000000 INFO @ Wed, 08 Dec 2021 21:33:41: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:33:44: 26000000 INFO @ Wed, 08 Dec 2021 21:33:49: 27000000 INFO @ Wed, 08 Dec 2021 21:33:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:33:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:33:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.10_summits.bed INFO @ Wed, 08 Dec 2021 21:33:52: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (260 records, 4 fields): 269 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:33:54: 28000000 INFO @ Wed, 08 Dec 2021 21:33:59: 29000000 INFO @ Wed, 08 Dec 2021 21:34:03: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:34:03: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:34:03: #1 total tags in treatment: 13715961 INFO @ Wed, 08 Dec 2021 21:34:03: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:34:03: #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 21:34:04: #1 tags after filtering in treatment: 12701982 INFO @ Wed, 08 Dec 2021 21:34:04: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:34:04: #1 finished! INFO @ Wed, 08 Dec 2021 21:34:04: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:34:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:34:04: #2 number of paired peaks: 332 WARNING @ Wed, 08 Dec 2021 21:34:04: Fewer paired peaks (332) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 332 pairs to build model! INFO @ Wed, 08 Dec 2021 21:34:04: start model_add_line... INFO @ Wed, 08 Dec 2021 21:34:04: start X-correlation... INFO @ Wed, 08 Dec 2021 21:34:05: end of X-cor INFO @ Wed, 08 Dec 2021 21:34:05: #2 finished! INFO @ Wed, 08 Dec 2021 21:34:05: #2 predicted fragment length is 132 bps INFO @ Wed, 08 Dec 2021 21:34:05: #2 alternative fragment length(s) may be 3,132,150,173,176 bps INFO @ Wed, 08 Dec 2021 21:34:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.20_model.r INFO @ Wed, 08 Dec 2021 21:34:05: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:34:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:34:28: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:34:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:34:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:34:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976739/SRX8976739.20_summits.bed INFO @ Wed, 08 Dec 2021 21:34:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (187 records, 4 fields): 1 millis CompletedMACS2peakCalling