Job ID = 14521826 SRX = ERX4439549 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3169264 spots for ERR4501478/ERR4501478.sra Written 3169264 spots for ERR4501478/ERR4501478.sra 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: 00:03:18 3169264 reads; of these: 3169264 (100.00%) were paired; of these: 1583154 (49.95%) aligned concordantly 0 times 1306139 (41.21%) aligned concordantly exactly 1 time 279971 (8.83%) aligned concordantly >1 times ---- 1583154 pairs aligned concordantly 0 times; of these: 295275 (18.65%) aligned discordantly 1 time ---- 1287879 pairs aligned 0 times concordantly or discordantly; of these: 2575758 mates make up the pairs; of these: 2018789 (78.38%) aligned 0 times 251629 (9.77%) aligned exactly 1 time 305340 (11.85%) aligned >1 times 68.15% overall alignment rate Time searching: 00:03:18 Overall time: 00:03:18 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [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 chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 112704 / 1847047 = 0.0610 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 @ Sat, 15 Jan 2022 21:48:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 15 Jan 2022 21:48:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:48:15: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:48:21: 1000000 INFO @ Sat, 15 Jan 2022 21:48:27: 2000000 INFO @ Sat, 15 Jan 2022 21:48:33: 3000000 INFO @ Sat, 15 Jan 2022 21:48:39: 4000000 INFO @ Sat, 15 Jan 2022 21:48:40: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:48:40: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:48:40: #1 total tags in treatment: 1493725 INFO @ Sat, 15 Jan 2022 21:48:40: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:48:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 21:48:40: #1 tags after filtering in treatment: 1175951 INFO @ Sat, 15 Jan 2022 21:48:40: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 21:48:40: #1 finished! INFO @ Sat, 15 Jan 2022 21:48:40: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:48:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:48:40: #2 number of paired peaks: 243 WARNING @ Sat, 15 Jan 2022 21:48:40: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Sat, 15 Jan 2022 21:48:40: start model_add_line... INFO @ Sat, 15 Jan 2022 21:48:40: start X-correlation... INFO @ Sat, 15 Jan 2022 21:48:40: end of X-cor INFO @ Sat, 15 Jan 2022 21:48:40: #2 finished! INFO @ Sat, 15 Jan 2022 21:48:40: #2 predicted fragment length is 160 bps INFO @ Sat, 15 Jan 2022 21:48:40: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 15 Jan 2022 21:48:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.05_model.r WARNING @ Sat, 15 Jan 2022 21:48:40: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:48:40: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Sat, 15 Jan 2022 21:48:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 21:48:40: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:48:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:48:43: #3 Call peaks for each chromosome... 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 @ Sat, 15 Jan 2022 21:48:44: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:48:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:48:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.05_summits.bed INFO @ Sat, 15 Jan 2022 21:48:44: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (867 records, 4 fields): 75 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:48:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 15 Jan 2022 21:48:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:48:45: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:48:52: 1000000 INFO @ Sat, 15 Jan 2022 21:48:59: 2000000 INFO @ Sat, 15 Jan 2022 21:49:05: 3000000 INFO @ Sat, 15 Jan 2022 21:49:11: 4000000 INFO @ Sat, 15 Jan 2022 21:49:12: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:49:12: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:49:12: #1 total tags in treatment: 1493725 INFO @ Sat, 15 Jan 2022 21:49:12: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:49:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 21:49:12: #1 tags after filtering in treatment: 1175951 INFO @ Sat, 15 Jan 2022 21:49:12: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 21:49:12: #1 finished! INFO @ Sat, 15 Jan 2022 21:49:12: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:49:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:49:12: #2 number of paired peaks: 243 WARNING @ Sat, 15 Jan 2022 21:49:12: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Sat, 15 Jan 2022 21:49:12: start model_add_line... INFO @ Sat, 15 Jan 2022 21:49:12: start X-correlation... INFO @ Sat, 15 Jan 2022 21:49:12: end of X-cor INFO @ Sat, 15 Jan 2022 21:49:12: #2 finished! INFO @ Sat, 15 Jan 2022 21:49:12: #2 predicted fragment length is 160 bps INFO @ Sat, 15 Jan 2022 21:49:12: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 15 Jan 2022 21:49:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.10_model.r WARNING @ Sat, 15 Jan 2022 21:49:12: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:49:12: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Sat, 15 Jan 2022 21:49:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 21:49:12: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:49:12: #3 Pre-compute pvalue-qvalue table... 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 @ Sat, 15 Jan 2022 21:49:15: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:49:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.bam'] # control file = None # effective genome size = 1.21e+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 @ Sat, 15 Jan 2022 21:49:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:49:15: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:49:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:49:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:49:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.10_summits.bed INFO @ Sat, 15 Jan 2022 21:49:16: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (611 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:49:22: 1000000 INFO @ Sat, 15 Jan 2022 21:49:30: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:49:37: 3000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:49:44: 4000000 INFO @ Sat, 15 Jan 2022 21:49:45: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:49:45: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:49:45: #1 total tags in treatment: 1493725 INFO @ Sat, 15 Jan 2022 21:49:45: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:49:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 21:49:45: #1 tags after filtering in treatment: 1175951 INFO @ Sat, 15 Jan 2022 21:49:45: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 15 Jan 2022 21:49:45: #1 finished! INFO @ Sat, 15 Jan 2022 21:49:45: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:49:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:49:45: #2 number of paired peaks: 243 WARNING @ Sat, 15 Jan 2022 21:49:45: Fewer paired peaks (243) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 243 pairs to build model! INFO @ Sat, 15 Jan 2022 21:49:45: start model_add_line... INFO @ Sat, 15 Jan 2022 21:49:45: start X-correlation... INFO @ Sat, 15 Jan 2022 21:49:45: end of X-cor INFO @ Sat, 15 Jan 2022 21:49:45: #2 finished! INFO @ Sat, 15 Jan 2022 21:49:45: #2 predicted fragment length is 160 bps INFO @ Sat, 15 Jan 2022 21:49:45: #2 alternative fragment length(s) may be 160 bps INFO @ Sat, 15 Jan 2022 21:49:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.20_model.r WARNING @ Sat, 15 Jan 2022 21:49:45: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:49:45: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Sat, 15 Jan 2022 21:49:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 21:49:45: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:49:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:49:48: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:49:49: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:49:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:49:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439549/ERX4439549.20_summits.bed INFO @ Sat, 15 Jan 2022 21:49:49: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (433 records, 4 fields): 1 millis CompletedMACS2peakCalling