Job ID = 14521821 SRX = ERX4439544 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3439438 spots for ERR4501473/ERR4501473.sra Written 3439438 spots for ERR4501473/ERR4501473.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: 00:02:39 3439438 reads; of these: 3439438 (100.00%) were paired; of these: 1089601 (31.68%) aligned concordantly 0 times 2016605 (58.63%) aligned concordantly exactly 1 time 333232 (9.69%) aligned concordantly >1 times ---- 1089601 pairs aligned concordantly 0 times; of these: 464618 (42.64%) aligned discordantly 1 time ---- 624983 pairs aligned 0 times concordantly or discordantly; of these: 1249966 mates make up the pairs; of these: 1021178 (81.70%) aligned 0 times 67256 (5.38%) aligned exactly 1 time 161532 (12.92%) aligned >1 times 85.15% overall alignment rate Time searching: 00:02:40 Overall time: 00:02:40 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 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] 43710 / 2783334 = 0.0157 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 21:47:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.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 21:47:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:47:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:47:19: 1000000 INFO @ Sat, 15 Jan 2022 21:47:25: 2000000 INFO @ Sat, 15 Jan 2022 21:47:31: 3000000 INFO @ Sat, 15 Jan 2022 21:47:37: 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 21:47:43: 5000000 INFO @ Sat, 15 Jan 2022 21:47:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.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 21:47:43: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:47:43: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:47:48: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:47:48: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:47:48: #1 total tags in treatment: 2314623 INFO @ Sat, 15 Jan 2022 21:47:48: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:47:48: #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 21:47:48: #1 tags after filtering in treatment: 2021026 INFO @ Sat, 15 Jan 2022 21:47:48: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Jan 2022 21:47:48: #1 finished! INFO @ Sat, 15 Jan 2022 21:47:48: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:47:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:47:48: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 21:47:48: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 21:47:48: start model_add_line... INFO @ Sat, 15 Jan 2022 21:47:48: start X-correlation... INFO @ Sat, 15 Jan 2022 21:47:48: end of X-cor INFO @ Sat, 15 Jan 2022 21:47:48: #2 finished! INFO @ Sat, 15 Jan 2022 21:47:48: #2 predicted fragment length is 163 bps INFO @ Sat, 15 Jan 2022 21:47:48: #2 alternative fragment length(s) may be 2,163,180,550 bps INFO @ Sat, 15 Jan 2022 21:47:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.05_model.r WARNING @ Sat, 15 Jan 2022 21:47:48: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:47:48: #2 You may need to consider one of the other alternative d(s): 2,163,180,550 WARNING @ Sat, 15 Jan 2022 21:47:48: #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 21:47:48: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:47:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:47:49: 1000000 INFO @ Sat, 15 Jan 2022 21:47:52: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:47:54: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:47:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:47:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.05_summits.bed INFO @ Sat, 15 Jan 2022 21:47:54: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (51 records, 4 fields): 73 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:47:56: 2000000 INFO @ Sat, 15 Jan 2022 21:48:02: 3000000 INFO @ Sat, 15 Jan 2022 21:48:08: 4000000 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 21:48:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.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 21:48:13: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:48:13: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:48:14: 5000000 INFO @ Sat, 15 Jan 2022 21:48:19: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:48:19: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:48:19: #1 total tags in treatment: 2314623 INFO @ Sat, 15 Jan 2022 21:48:19: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:48:19: #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 21:48:19: #1 tags after filtering in treatment: 2021026 INFO @ Sat, 15 Jan 2022 21:48:19: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Jan 2022 21:48:19: #1 finished! INFO @ Sat, 15 Jan 2022 21:48:19: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:48:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:48:19: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 21:48:19: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 21:48:19: start model_add_line... INFO @ Sat, 15 Jan 2022 21:48:19: start X-correlation... INFO @ Sat, 15 Jan 2022 21:48:19: end of X-cor INFO @ Sat, 15 Jan 2022 21:48:19: #2 finished! INFO @ Sat, 15 Jan 2022 21:48:19: #2 predicted fragment length is 163 bps INFO @ Sat, 15 Jan 2022 21:48:19: #2 alternative fragment length(s) may be 2,163,180,550 bps INFO @ Sat, 15 Jan 2022 21:48:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.10_model.r WARNING @ Sat, 15 Jan 2022 21:48:19: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:48:19: #2 You may need to consider one of the other alternative d(s): 2,163,180,550 WARNING @ Sat, 15 Jan 2022 21:48:19: #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 21:48:19: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:48:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:48:20: 1000000 INFO @ Sat, 15 Jan 2022 21:48:23: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:48:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:48:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:48:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.10_summits.bed INFO @ Sat, 15 Jan 2022 21:48:25: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (25 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:48:26: 2000000 INFO @ Sat, 15 Jan 2022 21:48:32: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:48:38: 4000000 INFO @ Sat, 15 Jan 2022 21:48:45: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:48:50: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:48:50: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:48:50: #1 total tags in treatment: 2314623 INFO @ Sat, 15 Jan 2022 21:48:50: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:48:50: #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 21:48:50: #1 tags after filtering in treatment: 2021026 INFO @ Sat, 15 Jan 2022 21:48:50: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Jan 2022 21:48:50: #1 finished! INFO @ Sat, 15 Jan 2022 21:48:50: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:48:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:48:50: #2 number of paired peaks: 171 WARNING @ Sat, 15 Jan 2022 21:48:50: Fewer paired peaks (171) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 171 pairs to build model! INFO @ Sat, 15 Jan 2022 21:48:50: start model_add_line... INFO @ Sat, 15 Jan 2022 21:48:50: start X-correlation... INFO @ Sat, 15 Jan 2022 21:48:50: end of X-cor INFO @ Sat, 15 Jan 2022 21:48:50: #2 finished! INFO @ Sat, 15 Jan 2022 21:48:50: #2 predicted fragment length is 163 bps INFO @ Sat, 15 Jan 2022 21:48:50: #2 alternative fragment length(s) may be 2,163,180,550 bps INFO @ Sat, 15 Jan 2022 21:48:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.20_model.r WARNING @ Sat, 15 Jan 2022 21:48:50: #2 Since the d (163) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:48:50: #2 You may need to consider one of the other alternative d(s): 2,163,180,550 WARNING @ Sat, 15 Jan 2022 21:48:50: #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 21:48:50: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:48:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:48:54: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:48:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:48:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:48:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439544/ERX4439544.20_summits.bed INFO @ Sat, 15 Jan 2022 21:48:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (11 records, 4 fields): 1 millis CompletedMACS2peakCalling