Job ID = 14158788 SRX = SRX10342582 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: 00:10:02 14917389 reads; of these: 14917389 (100.00%) were paired; of these: 2364683 (15.85%) aligned concordantly 0 times 10881236 (72.94%) aligned concordantly exactly 1 time 1671470 (11.20%) aligned concordantly >1 times ---- 2364683 pairs aligned concordantly 0 times; of these: 1808786 (76.49%) aligned discordantly 1 time ---- 555897 pairs aligned 0 times concordantly or discordantly; of these: 1111794 mates make up the pairs; of these: 338933 (30.49%) aligned 0 times 311767 (28.04%) aligned exactly 1 time 461094 (41.47%) aligned >1 times 98.86% overall alignment rate Time searching: 00:10:02 Overall time: 00:10:02 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 8 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] 757464 / 14343351 = 0.0528 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 18:08:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.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 18:08:50: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:08:50: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:08:54: 1000000 INFO @ Wed, 08 Dec 2021 18:08:58: 2000000 INFO @ Wed, 08 Dec 2021 18:09:02: 3000000 INFO @ Wed, 08 Dec 2021 18:09:05: 4000000 INFO @ Wed, 08 Dec 2021 18:09:09: 5000000 INFO @ Wed, 08 Dec 2021 18:09:13: 6000000 INFO @ Wed, 08 Dec 2021 18:09:17: 7000000 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 18:09:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.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 18:09:20: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:09:20: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:09:20: 8000000 INFO @ Wed, 08 Dec 2021 18:09:23: 1000000 INFO @ Wed, 08 Dec 2021 18:09:24: 9000000 INFO @ Wed, 08 Dec 2021 18:09:27: 2000000 INFO @ Wed, 08 Dec 2021 18:09:28: 10000000 INFO @ Wed, 08 Dec 2021 18:09:31: 3000000 INFO @ Wed, 08 Dec 2021 18:09:32: 11000000 INFO @ Wed, 08 Dec 2021 18:09:35: 4000000 INFO @ Wed, 08 Dec 2021 18:09:36: 12000000 INFO @ Wed, 08 Dec 2021 18:09:39: 5000000 INFO @ Wed, 08 Dec 2021 18:09:40: 13000000 INFO @ Wed, 08 Dec 2021 18:09:43: 6000000 INFO @ Wed, 08 Dec 2021 18:09:44: 14000000 INFO @ Wed, 08 Dec 2021 18:09:46: 7000000 INFO @ Wed, 08 Dec 2021 18:09:47: 15000000 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 18:09:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.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 18:09:50: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:09:50: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:09:50: 8000000 INFO @ Wed, 08 Dec 2021 18:09:51: 16000000 INFO @ Wed, 08 Dec 2021 18:09:53: 1000000 INFO @ Wed, 08 Dec 2021 18:09:54: 9000000 INFO @ Wed, 08 Dec 2021 18:09:55: 17000000 INFO @ Wed, 08 Dec 2021 18:09:57: 2000000 INFO @ Wed, 08 Dec 2021 18:09:58: 10000000 INFO @ Wed, 08 Dec 2021 18:09:59: 18000000 INFO @ Wed, 08 Dec 2021 18:10:01: 3000000 INFO @ Wed, 08 Dec 2021 18:10:02: 11000000 INFO @ Wed, 08 Dec 2021 18:10:03: 19000000 INFO @ Wed, 08 Dec 2021 18:10:05: 4000000 INFO @ Wed, 08 Dec 2021 18:10:05: 12000000 INFO @ Wed, 08 Dec 2021 18:10:07: 20000000 INFO @ Wed, 08 Dec 2021 18:10:09: 5000000 INFO @ Wed, 08 Dec 2021 18:10:09: 13000000 INFO @ Wed, 08 Dec 2021 18:10:11: 21000000 INFO @ Wed, 08 Dec 2021 18:10:13: 6000000 INFO @ Wed, 08 Dec 2021 18:10:13: 14000000 INFO @ Wed, 08 Dec 2021 18:10:14: 22000000 INFO @ Wed, 08 Dec 2021 18:10:16: 7000000 INFO @ Wed, 08 Dec 2021 18:10:17: 15000000 INFO @ Wed, 08 Dec 2021 18:10:18: 23000000 INFO @ Wed, 08 Dec 2021 18:10:20: 8000000 INFO @ Wed, 08 Dec 2021 18:10:21: 16000000 INFO @ Wed, 08 Dec 2021 18:10:22: 24000000 INFO @ Wed, 08 Dec 2021 18:10:24: 9000000 INFO @ Wed, 08 Dec 2021 18:10:25: 17000000 INFO @ Wed, 08 Dec 2021 18:10:26: 25000000 INFO @ Wed, 08 Dec 2021 18:10:28: 10000000 INFO @ Wed, 08 Dec 2021 18:10:28: 18000000 INFO @ Wed, 08 Dec 2021 18:10:30: 26000000 INFO @ Wed, 08 Dec 2021 18:10:32: 11000000 INFO @ Wed, 08 Dec 2021 18:10:32: 19000000 INFO @ Wed, 08 Dec 2021 18:10:33: 27000000 INFO @ Wed, 08 Dec 2021 18:10:35: 12000000 INFO @ Wed, 08 Dec 2021 18:10:36: 20000000 INFO @ Wed, 08 Dec 2021 18:10:37: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:10:37: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:10:37: #1 total tags in treatment: 11869529 INFO @ Wed, 08 Dec 2021 18:10:37: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:10:37: #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 18:10:37: #1 tags after filtering in treatment: 10970308 INFO @ Wed, 08 Dec 2021 18:10:37: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 18:10:37: #1 finished! INFO @ Wed, 08 Dec 2021 18:10:37: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:10:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:10:38: #2 number of paired peaks: 387 WARNING @ Wed, 08 Dec 2021 18:10:38: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Wed, 08 Dec 2021 18:10:38: start model_add_line... INFO @ Wed, 08 Dec 2021 18:10:38: start X-correlation... INFO @ Wed, 08 Dec 2021 18:10:38: end of X-cor INFO @ Wed, 08 Dec 2021 18:10:38: #2 finished! INFO @ Wed, 08 Dec 2021 18:10:38: #2 predicted fragment length is 158 bps INFO @ Wed, 08 Dec 2021 18:10:38: #2 alternative fragment length(s) may be 4,158 bps INFO @ Wed, 08 Dec 2021 18:10:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.05_model.r INFO @ Wed, 08 Dec 2021 18:10:38: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:10:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:10:39: 13000000 INFO @ Wed, 08 Dec 2021 18:10:40: 21000000 INFO @ Wed, 08 Dec 2021 18:10:43: 14000000 INFO @ Wed, 08 Dec 2021 18:10:44: 22000000 INFO @ Wed, 08 Dec 2021 18:10:47: 15000000 INFO @ Wed, 08 Dec 2021 18:10:47: 23000000 INFO @ Wed, 08 Dec 2021 18:10:51: 16000000 INFO @ Wed, 08 Dec 2021 18:10:51: 24000000 INFO @ Wed, 08 Dec 2021 18:10:54: 17000000 INFO @ Wed, 08 Dec 2021 18:10:55: 25000000 INFO @ Wed, 08 Dec 2021 18:10:58: 18000000 INFO @ Wed, 08 Dec 2021 18:10:59: 26000000 INFO @ Wed, 08 Dec 2021 18:11:00: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:11:02: 19000000 INFO @ Wed, 08 Dec 2021 18:11:02: 27000000 INFO @ Wed, 08 Dec 2021 18:11:06: 20000000 INFO @ Wed, 08 Dec 2021 18:11:06: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:11:06: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:11:06: #1 total tags in treatment: 11869529 INFO @ Wed, 08 Dec 2021 18:11:06: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:11:06: #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 18:11:06: #1 tags after filtering in treatment: 10970308 INFO @ Wed, 08 Dec 2021 18:11:06: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 18:11:06: #1 finished! INFO @ Wed, 08 Dec 2021 18:11:06: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:11:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:11:07: #2 number of paired peaks: 387 WARNING @ Wed, 08 Dec 2021 18:11:07: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Wed, 08 Dec 2021 18:11:07: start model_add_line... INFO @ Wed, 08 Dec 2021 18:11:07: start X-correlation... INFO @ Wed, 08 Dec 2021 18:11:07: end of X-cor INFO @ Wed, 08 Dec 2021 18:11:07: #2 finished! INFO @ Wed, 08 Dec 2021 18:11:07: #2 predicted fragment length is 158 bps INFO @ Wed, 08 Dec 2021 18:11:07: #2 alternative fragment length(s) may be 4,158 bps INFO @ Wed, 08 Dec 2021 18:11:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.10_model.r INFO @ Wed, 08 Dec 2021 18:11:07: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:11:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:11:09: 21000000 INFO @ Wed, 08 Dec 2021 18:11:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:11:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:11:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.05_summits.bed INFO @ Wed, 08 Dec 2021 18:11:10: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (346 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:11:13: 22000000 INFO @ Wed, 08 Dec 2021 18:11:17: 23000000 INFO @ Wed, 08 Dec 2021 18:11:21: 24000000 INFO @ Wed, 08 Dec 2021 18:11:24: 25000000 INFO @ Wed, 08 Dec 2021 18:11:28: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:11:28: 26000000 INFO @ Wed, 08 Dec 2021 18:11:32: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:11:36: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:11:36: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:11:36: #1 total tags in treatment: 11869529 INFO @ Wed, 08 Dec 2021 18:11:36: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:11:36: #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 18:11:36: #1 tags after filtering in treatment: 10970308 INFO @ Wed, 08 Dec 2021 18:11:36: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 18:11:36: #1 finished! INFO @ Wed, 08 Dec 2021 18:11:36: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:11:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:11:37: #2 number of paired peaks: 387 WARNING @ Wed, 08 Dec 2021 18:11:37: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Wed, 08 Dec 2021 18:11:37: start model_add_line... INFO @ Wed, 08 Dec 2021 18:11:37: start X-correlation... INFO @ Wed, 08 Dec 2021 18:11:37: end of X-cor INFO @ Wed, 08 Dec 2021 18:11:37: #2 finished! INFO @ Wed, 08 Dec 2021 18:11:37: #2 predicted fragment length is 158 bps INFO @ Wed, 08 Dec 2021 18:11:37: #2 alternative fragment length(s) may be 4,158 bps INFO @ Wed, 08 Dec 2021 18:11:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.20_model.r INFO @ Wed, 08 Dec 2021 18:11:37: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:11:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:11:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:11:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:11:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.10_summits.bed INFO @ Wed, 08 Dec 2021 18:11:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (263 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:11:58: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:12:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:12:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:12:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342582/SRX10342582.20_summits.bed INFO @ Wed, 08 Dec 2021 18:12:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (179 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。