Job ID = 14521682 SRX = ERX4439612 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3442037 spots for ERR4501541/ERR4501541.sra Written 3442037 spots for ERR4501541/ERR4501541.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: 00:04:06 3442037 reads; of these: 3442037 (100.00%) were paired; of these: 845277 (24.56%) aligned concordantly 0 times 2095384 (60.88%) aligned concordantly exactly 1 time 501376 (14.57%) aligned concordantly >1 times ---- 845277 pairs aligned concordantly 0 times; of these: 345046 (40.82%) aligned discordantly 1 time ---- 500231 pairs aligned 0 times concordantly or discordantly; of these: 1000462 mates make up the pairs; of these: 777265 (77.69%) aligned 0 times 51429 (5.14%) aligned exactly 1 time 171768 (17.17%) aligned >1 times 88.71% overall alignment rate Time searching: 00:04:06 Overall time: 00:04:06 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] 122429 / 2915827 = 0.0420 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 21:32:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.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 21:32:43: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:32:43: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:32:51: 1000000 INFO @ Sat, 15 Jan 2022 21:32:57: 2000000 INFO @ Sat, 15 Jan 2022 21:33:04: 3000000 INFO @ Sat, 15 Jan 2022 21:33:11: 4000000 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 21:33:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.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 21:33:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:33:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:33:18: 5000000 INFO @ Sat, 15 Jan 2022 21:33:21: 1000000 INFO @ Sat, 15 Jan 2022 21:33:24: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:33:24: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:33:24: #1 total tags in treatment: 2492469 INFO @ Sat, 15 Jan 2022 21:33:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:33:24: #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 21:33:24: #1 tags after filtering in treatment: 1824573 INFO @ Sat, 15 Jan 2022 21:33:24: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:33:24: #1 finished! INFO @ Sat, 15 Jan 2022 21:33:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:33:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:33:24: #2 number of paired peaks: 264 WARNING @ Sat, 15 Jan 2022 21:33:24: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Sat, 15 Jan 2022 21:33:24: start model_add_line... INFO @ Sat, 15 Jan 2022 21:33:24: start X-correlation... INFO @ Sat, 15 Jan 2022 21:33:24: end of X-cor INFO @ Sat, 15 Jan 2022 21:33:24: #2 finished! INFO @ Sat, 15 Jan 2022 21:33:24: #2 predicted fragment length is 172 bps INFO @ Sat, 15 Jan 2022 21:33:24: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 15 Jan 2022 21:33:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.05_model.r WARNING @ Sat, 15 Jan 2022 21:33:24: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:33:24: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Sat, 15 Jan 2022 21:33:24: #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 21:33:24: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:33:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:33:29: 2000000 INFO @ Sat, 15 Jan 2022 21:33:30: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:33:32: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:33:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:33:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.05_summits.bed INFO @ Sat, 15 Jan 2022 21:33:32: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1441 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:33:37: 3000000 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 21:33:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.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 21:33:43: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:33:43: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:33:44: 4000000 INFO @ Sat, 15 Jan 2022 21:33:51: 1000000 INFO @ Sat, 15 Jan 2022 21:33:52: 5000000 INFO @ Sat, 15 Jan 2022 21:33:58: 2000000 INFO @ Sat, 15 Jan 2022 21:33:59: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:33:59: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:33:59: #1 total tags in treatment: 2492469 INFO @ Sat, 15 Jan 2022 21:33:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:33:59: #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 21:33:59: #1 tags after filtering in treatment: 1824573 INFO @ Sat, 15 Jan 2022 21:33:59: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:33:59: #1 finished! INFO @ Sat, 15 Jan 2022 21:33:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:33:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:33:59: #2 number of paired peaks: 264 WARNING @ Sat, 15 Jan 2022 21:33:59: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Sat, 15 Jan 2022 21:33:59: start model_add_line... INFO @ Sat, 15 Jan 2022 21:33:59: start X-correlation... INFO @ Sat, 15 Jan 2022 21:33:59: end of X-cor INFO @ Sat, 15 Jan 2022 21:33:59: #2 finished! INFO @ Sat, 15 Jan 2022 21:33:59: #2 predicted fragment length is 172 bps INFO @ Sat, 15 Jan 2022 21:33:59: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 15 Jan 2022 21:33:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.10_model.r WARNING @ Sat, 15 Jan 2022 21:33:59: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:33:59: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Sat, 15 Jan 2022 21:33:59: #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 21:33:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:33:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:34:05: 3000000 INFO @ Sat, 15 Jan 2022 21:34:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:34:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:34:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:34:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.10_summits.bed INFO @ Sat, 15 Jan 2022 21:34:07: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (1048 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:34:11: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:34:18: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:34:25: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:34:25: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:34:25: #1 total tags in treatment: 2492469 INFO @ Sat, 15 Jan 2022 21:34:25: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:34:25: #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 21:34:25: #1 tags after filtering in treatment: 1824573 INFO @ Sat, 15 Jan 2022 21:34:25: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:34:25: #1 finished! INFO @ Sat, 15 Jan 2022 21:34:25: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:34:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:34:25: #2 number of paired peaks: 264 WARNING @ Sat, 15 Jan 2022 21:34:25: Fewer paired peaks (264) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 264 pairs to build model! INFO @ Sat, 15 Jan 2022 21:34:25: start model_add_line... INFO @ Sat, 15 Jan 2022 21:34:25: start X-correlation... INFO @ Sat, 15 Jan 2022 21:34:25: end of X-cor INFO @ Sat, 15 Jan 2022 21:34:25: #2 finished! INFO @ Sat, 15 Jan 2022 21:34:25: #2 predicted fragment length is 172 bps INFO @ Sat, 15 Jan 2022 21:34:25: #2 alternative fragment length(s) may be 172 bps INFO @ Sat, 15 Jan 2022 21:34:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.20_model.r WARNING @ Sat, 15 Jan 2022 21:34:25: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:34:25: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Sat, 15 Jan 2022 21:34:25: #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 21:34:25: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:34:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:34:31: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:34:33: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:34:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:34:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439612/ERX4439612.20_summits.bed INFO @ Sat, 15 Jan 2022 21:34:33: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (706 records, 4 fields): 6 millis CompletedMACS2peakCalling