Job ID = 14159287 SRX = SRX8976719 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: 00:10:40 12602747 reads; of these: 12602747 (100.00%) were paired; of these: 899411 (7.14%) aligned concordantly 0 times 9746189 (77.33%) aligned concordantly exactly 1 time 1957147 (15.53%) aligned concordantly >1 times ---- 899411 pairs aligned concordantly 0 times; of these: 511616 (56.88%) aligned discordantly 1 time ---- 387795 pairs aligned 0 times concordantly or discordantly; of these: 775590 mates make up the pairs; of these: 470203 (60.63%) aligned 0 times 125194 (16.14%) aligned exactly 1 time 180193 (23.23%) aligned >1 times 98.13% overall alignment rate Time searching: 00:10:40 Overall time: 00:10:40 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] 5540511 / 12210750 = 0.4537 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 20:53:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.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 20:53:48: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:53:48: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:53:53: 1000000 INFO @ Wed, 08 Dec 2021 20:53:58: 2000000 INFO @ Wed, 08 Dec 2021 20:54:02: 3000000 INFO @ Wed, 08 Dec 2021 20:54:07: 4000000 INFO @ Wed, 08 Dec 2021 20:54:11: 5000000 INFO @ Wed, 08 Dec 2021 20:54:16: 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 20:54:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.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 20:54:18: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:54:18: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:54:21: 7000000 INFO @ Wed, 08 Dec 2021 20:54:23: 1000000 INFO @ Wed, 08 Dec 2021 20:54:26: 8000000 INFO @ Wed, 08 Dec 2021 20:54:29: 2000000 INFO @ Wed, 08 Dec 2021 20:54:31: 9000000 INFO @ Wed, 08 Dec 2021 20:54:34: 3000000 INFO @ Wed, 08 Dec 2021 20:54:36: 10000000 INFO @ Wed, 08 Dec 2021 20:54:39: 4000000 INFO @ Wed, 08 Dec 2021 20:54:41: 11000000 INFO @ Wed, 08 Dec 2021 20:54:44: 5000000 INFO @ Wed, 08 Dec 2021 20:54:46: 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 20:54:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.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 20:54:48: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:54:48: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:54:49: 6000000 INFO @ Wed, 08 Dec 2021 20:54:51: 13000000 INFO @ Wed, 08 Dec 2021 20:54:53: 1000000 INFO @ Wed, 08 Dec 2021 20:54:54: 7000000 INFO @ Wed, 08 Dec 2021 20:54:55: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:54:55: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:54:55: #1 total tags in treatment: 6332369 INFO @ Wed, 08 Dec 2021 20:54:55: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:54:55: #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 20:54:55: #1 tags after filtering in treatment: 5914773 INFO @ Wed, 08 Dec 2021 20:54:55: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 20:54:55: #1 finished! INFO @ Wed, 08 Dec 2021 20:54:55: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:54:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:54:55: #2 number of paired peaks: 774 WARNING @ Wed, 08 Dec 2021 20:54:55: Fewer paired peaks (774) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 774 pairs to build model! INFO @ Wed, 08 Dec 2021 20:54:55: start model_add_line... INFO @ Wed, 08 Dec 2021 20:54:55: start X-correlation... INFO @ Wed, 08 Dec 2021 20:54:55: end of X-cor INFO @ Wed, 08 Dec 2021 20:54:55: #2 finished! INFO @ Wed, 08 Dec 2021 20:54:55: #2 predicted fragment length is 170 bps INFO @ Wed, 08 Dec 2021 20:54:55: #2 alternative fragment length(s) may be 4,170 bps INFO @ Wed, 08 Dec 2021 20:54:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.05_model.r INFO @ Wed, 08 Dec 2021 20:54:55: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:54:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:54:59: 2000000 INFO @ Wed, 08 Dec 2021 20:54:59: 8000000 INFO @ Wed, 08 Dec 2021 20:55:04: 3000000 INFO @ Wed, 08 Dec 2021 20:55:04: 9000000 INFO @ Wed, 08 Dec 2021 20:55:09: 4000000 INFO @ Wed, 08 Dec 2021 20:55:09: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:55:10: 10000000 INFO @ Wed, 08 Dec 2021 20:55:14: 5000000 INFO @ Wed, 08 Dec 2021 20:55:15: 11000000 INFO @ Wed, 08 Dec 2021 20:55:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:55:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:55:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.05_summits.bed INFO @ Wed, 08 Dec 2021 20:55:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (569 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:55:19: 6000000 INFO @ Wed, 08 Dec 2021 20:55:20: 12000000 INFO @ Wed, 08 Dec 2021 20:55:24: 7000000 INFO @ Wed, 08 Dec 2021 20:55:25: 13000000 INFO @ Wed, 08 Dec 2021 20:55:28: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:55:28: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:55:28: #1 total tags in treatment: 6332369 INFO @ Wed, 08 Dec 2021 20:55:28: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:55:28: #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 20:55:28: #1 tags after filtering in treatment: 5914773 INFO @ Wed, 08 Dec 2021 20:55:28: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 20:55:28: #1 finished! INFO @ Wed, 08 Dec 2021 20:55:28: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:55:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:55:29: #2 number of paired peaks: 774 WARNING @ Wed, 08 Dec 2021 20:55:29: Fewer paired peaks (774) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 774 pairs to build model! INFO @ Wed, 08 Dec 2021 20:55:29: start model_add_line... INFO @ Wed, 08 Dec 2021 20:55:29: start X-correlation... INFO @ Wed, 08 Dec 2021 20:55:29: end of X-cor INFO @ Wed, 08 Dec 2021 20:55:29: #2 finished! INFO @ Wed, 08 Dec 2021 20:55:29: #2 predicted fragment length is 170 bps INFO @ Wed, 08 Dec 2021 20:55:29: #2 alternative fragment length(s) may be 4,170 bps INFO @ Wed, 08 Dec 2021 20:55:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.10_model.r INFO @ Wed, 08 Dec 2021 20:55:29: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:55:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:55:29: 8000000 INFO @ Wed, 08 Dec 2021 20:55:34: 9000000 INFO @ Wed, 08 Dec 2021 20:55:39: 10000000 INFO @ Wed, 08 Dec 2021 20:55:43: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:55:44: 11000000 INFO @ Wed, 08 Dec 2021 20:55:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:55:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:55:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.10_summits.bed INFO @ Wed, 08 Dec 2021 20:55:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (323 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:55:49: 12000000 INFO @ Wed, 08 Dec 2021 20:55:54: 13000000 INFO @ Wed, 08 Dec 2021 20:55:58: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:55:58: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:55:58: #1 total tags in treatment: 6332369 INFO @ Wed, 08 Dec 2021 20:55:58: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:55:58: #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 20:55:58: #1 tags after filtering in treatment: 5914773 INFO @ Wed, 08 Dec 2021 20:55:58: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 20:55:58: #1 finished! INFO @ Wed, 08 Dec 2021 20:55:58: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:55:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:55:58: #2 number of paired peaks: 774 WARNING @ Wed, 08 Dec 2021 20:55:58: Fewer paired peaks (774) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 774 pairs to build model! INFO @ Wed, 08 Dec 2021 20:55:58: start model_add_line... INFO @ Wed, 08 Dec 2021 20:55:58: start X-correlation... INFO @ Wed, 08 Dec 2021 20:55:58: end of X-cor INFO @ Wed, 08 Dec 2021 20:55:58: #2 finished! INFO @ Wed, 08 Dec 2021 20:55:58: #2 predicted fragment length is 170 bps INFO @ Wed, 08 Dec 2021 20:55:58: #2 alternative fragment length(s) may be 4,170 bps INFO @ Wed, 08 Dec 2021 20:55:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.20_model.r INFO @ Wed, 08 Dec 2021 20:55:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:55:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:56:12: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:56:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:56:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:56:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976719/SRX8976719.20_summits.bed INFO @ Wed, 08 Dec 2021 20:56:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (210 records, 4 fields): 1 millis CompletedMACS2peakCalling