Job ID = 14159350 SRX = SRX8976737 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: 00:11:31 15306503 reads; of these: 15306503 (100.00%) were paired; of these: 316531 (2.07%) aligned concordantly 0 times 13060193 (85.32%) aligned concordantly exactly 1 time 1929779 (12.61%) aligned concordantly >1 times ---- 316531 pairs aligned concordantly 0 times; of these: 142446 (45.00%) aligned discordantly 1 time ---- 174085 pairs aligned 0 times concordantly or discordantly; of these: 348170 mates make up the pairs; of these: 180961 (51.97%) aligned 0 times 100271 (28.80%) aligned exactly 1 time 66938 (19.23%) aligned >1 times 99.41% overall alignment rate Time searching: 00:11:31 Overall time: 00:11:31 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 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] 453769 / 15089325 = 0.0301 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 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 21:31:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.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 21:31:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.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 21:31:04: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:31:04: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:31:04: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:31:04: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:31:08: 1000000 INFO @ Wed, 08 Dec 2021 21:31:08: 1000000 INFO @ Wed, 08 Dec 2021 21:31:13: 2000000 INFO @ Wed, 08 Dec 2021 21:31:13: 2000000 INFO @ Wed, 08 Dec 2021 21:31:19: 3000000 INFO @ Wed, 08 Dec 2021 21:31:19: 3000000 INFO @ Wed, 08 Dec 2021 21:31:24: 4000000 INFO @ Wed, 08 Dec 2021 21:31:24: 4000000 INFO @ Wed, 08 Dec 2021 21:31:30: 5000000 INFO @ Wed, 08 Dec 2021 21:31:30: 5000000 BedGraph に変換中... INFO @ Wed, 08 Dec 2021 21:31:36: 6000000 INFO @ Wed, 08 Dec 2021 21:31:36: 6000000 INFO @ Wed, 08 Dec 2021 21:31:42: 7000000 INFO @ Wed, 08 Dec 2021 21:31:42: 7000000 INFO @ Wed, 08 Dec 2021 21:31:47: 8000000 INFO @ Wed, 08 Dec 2021 21:31:47: 8000000 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 21:31:53: 9000000 INFO @ Wed, 08 Dec 2021 21:31:53: 9000000 INFO @ Wed, 08 Dec 2021 21:31:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.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 21:31:56: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:31:56: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:31:59: 10000000 INFO @ Wed, 08 Dec 2021 21:31:59: 10000000 INFO @ Wed, 08 Dec 2021 21:32:02: 1000000 INFO @ Wed, 08 Dec 2021 21:32:05: 11000000 INFO @ Wed, 08 Dec 2021 21:32:05: 11000000 INFO @ Wed, 08 Dec 2021 21:32:07: 2000000 INFO @ Wed, 08 Dec 2021 21:32:10: 12000000 INFO @ Wed, 08 Dec 2021 21:32:10: 12000000 INFO @ Wed, 08 Dec 2021 21:32:13: 3000000 INFO @ Wed, 08 Dec 2021 21:32:16: 13000000 INFO @ Wed, 08 Dec 2021 21:32:16: 13000000 INFO @ Wed, 08 Dec 2021 21:32:19: 4000000 INFO @ Wed, 08 Dec 2021 21:32:22: 14000000 INFO @ Wed, 08 Dec 2021 21:32:22: 14000000 INFO @ Wed, 08 Dec 2021 21:32:24: 5000000 INFO @ Wed, 08 Dec 2021 21:32:28: 15000000 INFO @ Wed, 08 Dec 2021 21:32:28: 15000000 INFO @ Wed, 08 Dec 2021 21:32:30: 6000000 INFO @ Wed, 08 Dec 2021 21:32:34: 16000000 INFO @ Wed, 08 Dec 2021 21:32:34: 16000000 INFO @ Wed, 08 Dec 2021 21:32:36: 7000000 INFO @ Wed, 08 Dec 2021 21:32:39: 17000000 INFO @ Wed, 08 Dec 2021 21:32:39: 17000000 INFO @ Wed, 08 Dec 2021 21:32:41: 8000000 INFO @ Wed, 08 Dec 2021 21:32:45: 18000000 INFO @ Wed, 08 Dec 2021 21:32:45: 18000000 INFO @ Wed, 08 Dec 2021 21:32:47: 9000000 INFO @ Wed, 08 Dec 2021 21:32:50: 19000000 INFO @ Wed, 08 Dec 2021 21:32:51: 19000000 INFO @ Wed, 08 Dec 2021 21:32:52: 10000000 INFO @ Wed, 08 Dec 2021 21:32:56: 20000000 INFO @ Wed, 08 Dec 2021 21:32:56: 20000000 INFO @ Wed, 08 Dec 2021 21:32:58: 11000000 INFO @ Wed, 08 Dec 2021 21:33:01: 21000000 INFO @ Wed, 08 Dec 2021 21:33:02: 21000000 INFO @ Wed, 08 Dec 2021 21:33:04: 12000000 INFO @ Wed, 08 Dec 2021 21:33:06: 22000000 INFO @ Wed, 08 Dec 2021 21:33:07: 22000000 INFO @ Wed, 08 Dec 2021 21:33:09: 13000000 INFO @ Wed, 08 Dec 2021 21:33:11: 23000000 INFO @ Wed, 08 Dec 2021 21:33:12: 23000000 INFO @ Wed, 08 Dec 2021 21:33:15: 14000000 INFO @ Wed, 08 Dec 2021 21:33:16: 24000000 INFO @ Wed, 08 Dec 2021 21:33:17: 24000000 INFO @ Wed, 08 Dec 2021 21:33:20: 15000000 INFO @ Wed, 08 Dec 2021 21:33:21: 25000000 INFO @ Wed, 08 Dec 2021 21:33:22: 25000000 INFO @ Wed, 08 Dec 2021 21:33:26: 26000000 INFO @ Wed, 08 Dec 2021 21:33:26: 16000000 INFO @ Wed, 08 Dec 2021 21:33:27: 26000000 BedGraph に変換しました。 INFO @ Wed, 08 Dec 2021 21:33:31: 27000000 INFO @ Wed, 08 Dec 2021 21:33:32: 17000000 INFO @ Wed, 08 Dec 2021 21:33:32: 27000000 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:33:35: 28000000 INFO @ Wed, 08 Dec 2021 21:33:37: 28000000 INFO @ Wed, 08 Dec 2021 21:33:38: 18000000 INFO @ Wed, 08 Dec 2021 21:33:40: 29000000 INFO @ Wed, 08 Dec 2021 21:33:42: 29000000 INFO @ Wed, 08 Dec 2021 21:33:43: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:33:43: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:33:43: #1 total tags in treatment: 14538581 INFO @ Wed, 08 Dec 2021 21:33:43: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:33:43: #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 21:33:43: #1 tags after filtering in treatment: 13439719 INFO @ Wed, 08 Dec 2021 21:33:43: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 21:33:43: #1 finished! INFO @ Wed, 08 Dec 2021 21:33:43: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:33:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:33:43: 19000000 INFO @ Wed, 08 Dec 2021 21:33:44: #2 number of paired peaks: 283 WARNING @ Wed, 08 Dec 2021 21:33:44: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Wed, 08 Dec 2021 21:33:44: start model_add_line... INFO @ Wed, 08 Dec 2021 21:33:44: start X-correlation... INFO @ Wed, 08 Dec 2021 21:33:44: end of X-cor INFO @ Wed, 08 Dec 2021 21:33:44: #2 finished! INFO @ Wed, 08 Dec 2021 21:33:44: #2 predicted fragment length is 124 bps INFO @ Wed, 08 Dec 2021 21:33:44: #2 alternative fragment length(s) may be 3,124,154,176 bps INFO @ Wed, 08 Dec 2021 21:33:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.05_model.r INFO @ Wed, 08 Dec 2021 21:33:44: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:33:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:33:45: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:33:45: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:33:45: #1 total tags in treatment: 14538581 INFO @ Wed, 08 Dec 2021 21:33:45: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:33:45: #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 21:33:45: #1 tags after filtering in treatment: 13439719 INFO @ Wed, 08 Dec 2021 21:33:45: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 21:33:45: #1 finished! INFO @ Wed, 08 Dec 2021 21:33:45: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:33:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:33:46: #2 number of paired peaks: 283 WARNING @ Wed, 08 Dec 2021 21:33:46: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Wed, 08 Dec 2021 21:33:46: start model_add_line... INFO @ Wed, 08 Dec 2021 21:33:46: start X-correlation... INFO @ Wed, 08 Dec 2021 21:33:46: end of X-cor INFO @ Wed, 08 Dec 2021 21:33:46: #2 finished! INFO @ Wed, 08 Dec 2021 21:33:46: #2 predicted fragment length is 124 bps INFO @ Wed, 08 Dec 2021 21:33:46: #2 alternative fragment length(s) may be 3,124,154,176 bps INFO @ Wed, 08 Dec 2021 21:33:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.10_model.r INFO @ Wed, 08 Dec 2021 21:33:46: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:33:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:33:49: 20000000 INFO @ Wed, 08 Dec 2021 21:33:54: 21000000 INFO @ Wed, 08 Dec 2021 21:34:00: 22000000 INFO @ Wed, 08 Dec 2021 21:34:05: 23000000 INFO @ Wed, 08 Dec 2021 21:34:10: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:34:10: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:34:11: 24000000 INFO @ Wed, 08 Dec 2021 21:34:16: 25000000 INFO @ Wed, 08 Dec 2021 21:34:24: 26000000 INFO @ Wed, 08 Dec 2021 21:34:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:34:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:34:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:34:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.10_summits.bed INFO @ Wed, 08 Dec 2021 21:34:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:34:27: Done! INFO @ Wed, 08 Dec 2021 21:34:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.05_summits.bed INFO @ Wed, 08 Dec 2021 21:34:27: Done! pass1 - making usageList (7 chroms): 0 millis pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (354 records, 4 fields): 2 millis pass2 - checking and writing primary data (269 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:34:29: 27000000 INFO @ Wed, 08 Dec 2021 21:34:34: 28000000 INFO @ Wed, 08 Dec 2021 21:34:39: 29000000 INFO @ Wed, 08 Dec 2021 21:34:42: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:34:42: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:34:42: #1 total tags in treatment: 14538581 INFO @ Wed, 08 Dec 2021 21:34:42: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:34:42: #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 21:34:42: #1 tags after filtering in treatment: 13439719 INFO @ Wed, 08 Dec 2021 21:34:42: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 21:34:42: #1 finished! INFO @ Wed, 08 Dec 2021 21:34:42: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:34:42: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:34:43: #2 number of paired peaks: 283 WARNING @ Wed, 08 Dec 2021 21:34:43: Fewer paired peaks (283) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 283 pairs to build model! INFO @ Wed, 08 Dec 2021 21:34:43: start model_add_line... INFO @ Wed, 08 Dec 2021 21:34:43: start X-correlation... INFO @ Wed, 08 Dec 2021 21:34:43: end of X-cor INFO @ Wed, 08 Dec 2021 21:34:43: #2 finished! INFO @ Wed, 08 Dec 2021 21:34:43: #2 predicted fragment length is 124 bps INFO @ Wed, 08 Dec 2021 21:34:43: #2 alternative fragment length(s) may be 3,124,154,176 bps INFO @ Wed, 08 Dec 2021 21:34:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.20_model.r INFO @ Wed, 08 Dec 2021 21:34:43: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:34:43: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:35:08: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:35:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:35:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:35:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976737/SRX8976737.20_summits.bed INFO @ Wed, 08 Dec 2021 21:35:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (167 records, 4 fields): 1 millis CompletedMACS2peakCalling