Job ID = 14521715 SRX = ERX4439625 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3269572 spots for ERR4501554/ERR4501554.sra Written 3269572 spots for ERR4501554/ERR4501554.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 3269572 reads; of these: 3269572 (100.00%) were paired; of these: 730590 (22.35%) aligned concordantly 0 times 2300713 (70.37%) aligned concordantly exactly 1 time 238269 (7.29%) aligned concordantly >1 times ---- 730590 pairs aligned concordantly 0 times; of these: 351922 (48.17%) aligned discordantly 1 time ---- 378668 pairs aligned 0 times concordantly or discordantly; of these: 757336 mates make up the pairs; of these: 629058 (83.06%) aligned 0 times 51584 (6.81%) aligned exactly 1 time 76694 (10.13%) aligned >1 times 90.38% overall alignment rate Time searching: 00:02:39 Overall time: 00:02:39 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] 41274 / 2867604 = 0.0144 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 21:36:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.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 21:36:16: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:36:16: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:36:23: 1000000 INFO @ Sat, 15 Jan 2022 21:36:29: 2000000 INFO @ Sat, 15 Jan 2022 21:36:36: 3000000 INFO @ Sat, 15 Jan 2022 21:36:42: 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 21:36:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.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 21:36:46: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:36:46: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:36:50: 5000000 INFO @ Sat, 15 Jan 2022 21:36:55: 1000000 INFO @ Sat, 15 Jan 2022 21:36:58: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:36:58: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:36:58: #1 total tags in treatment: 2506042 INFO @ Sat, 15 Jan 2022 21:36:58: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:36:58: #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 21:36:58: #1 tags after filtering in treatment: 2097778 INFO @ Sat, 15 Jan 2022 21:36:58: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 15 Jan 2022 21:36:58: #1 finished! INFO @ Sat, 15 Jan 2022 21:36:58: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:36:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:36:58: #2 number of paired peaks: 137 WARNING @ Sat, 15 Jan 2022 21:36:58: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Sat, 15 Jan 2022 21:36:58: start model_add_line... INFO @ Sat, 15 Jan 2022 21:36:58: start X-correlation... INFO @ Sat, 15 Jan 2022 21:36:58: end of X-cor INFO @ Sat, 15 Jan 2022 21:36:58: #2 finished! INFO @ Sat, 15 Jan 2022 21:36:58: #2 predicted fragment length is 195 bps INFO @ Sat, 15 Jan 2022 21:36:58: #2 alternative fragment length(s) may be 195 bps INFO @ Sat, 15 Jan 2022 21:36:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.05_model.r WARNING @ Sat, 15 Jan 2022 21:36:58: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:36:58: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Sat, 15 Jan 2022 21:36:58: #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 21:36:58: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:36:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:37:04: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:37:04: 2000000 INFO @ Sat, 15 Jan 2022 21:37:06: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:37:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:37:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.05_summits.bed INFO @ Sat, 15 Jan 2022 21:37:06: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (1340 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:37:13: 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 21:37:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.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 21:37:16: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:37:16: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:37:22: 4000000 INFO @ Sat, 15 Jan 2022 21:37:26: 1000000 INFO @ Sat, 15 Jan 2022 21:37:31: 5000000 INFO @ Sat, 15 Jan 2022 21:37:35: 2000000 INFO @ Sat, 15 Jan 2022 21:37:38: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:37:38: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:37:38: #1 total tags in treatment: 2506042 INFO @ Sat, 15 Jan 2022 21:37:38: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:37:38: #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 21:37:39: #1 tags after filtering in treatment: 2097778 INFO @ Sat, 15 Jan 2022 21:37:39: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 15 Jan 2022 21:37:39: #1 finished! INFO @ Sat, 15 Jan 2022 21:37:39: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:37:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:37:39: #2 number of paired peaks: 137 WARNING @ Sat, 15 Jan 2022 21:37:39: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Sat, 15 Jan 2022 21:37:39: start model_add_line... INFO @ Sat, 15 Jan 2022 21:37:39: start X-correlation... INFO @ Sat, 15 Jan 2022 21:37:39: end of X-cor INFO @ Sat, 15 Jan 2022 21:37:39: #2 finished! INFO @ Sat, 15 Jan 2022 21:37:39: #2 predicted fragment length is 195 bps INFO @ Sat, 15 Jan 2022 21:37:39: #2 alternative fragment length(s) may be 195 bps INFO @ Sat, 15 Jan 2022 21:37:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.10_model.r WARNING @ Sat, 15 Jan 2022 21:37:39: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:37:39: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Sat, 15 Jan 2022 21:37:39: #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 21:37:39: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:37:39: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:37:44: 3000000 INFO @ Sat, 15 Jan 2022 21:37:44: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:37:46: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:37:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:37:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.10_summits.bed INFO @ Sat, 15 Jan 2022 21:37:46: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (1018 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:37:52: 4000000 INFO @ Sat, 15 Jan 2022 21:38:01: 5000000 INFO @ Sat, 15 Jan 2022 21:38:07: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:38:07: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:38:07: #1 total tags in treatment: 2506042 INFO @ Sat, 15 Jan 2022 21:38:07: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:38:07: #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 21:38:07: #1 tags after filtering in treatment: 2097778 INFO @ Sat, 15 Jan 2022 21:38:07: #1 Redundant rate of treatment: 0.16 INFO @ Sat, 15 Jan 2022 21:38:07: #1 finished! INFO @ Sat, 15 Jan 2022 21:38:07: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:38:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:38:07: #2 number of paired peaks: 137 WARNING @ Sat, 15 Jan 2022 21:38:07: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Sat, 15 Jan 2022 21:38:07: start model_add_line... INFO @ Sat, 15 Jan 2022 21:38:07: start X-correlation... INFO @ Sat, 15 Jan 2022 21:38:07: end of X-cor INFO @ Sat, 15 Jan 2022 21:38:07: #2 finished! INFO @ Sat, 15 Jan 2022 21:38:07: #2 predicted fragment length is 195 bps INFO @ Sat, 15 Jan 2022 21:38:07: #2 alternative fragment length(s) may be 195 bps INFO @ Sat, 15 Jan 2022 21:38:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.20_model.r WARNING @ Sat, 15 Jan 2022 21:38:07: #2 Since the d (195) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:38:07: #2 You may need to consider one of the other alternative d(s): 195 WARNING @ Sat, 15 Jan 2022 21:38:07: #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 21:38:07: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:38:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:38:13: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:38:14: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:38:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:38:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439625/ERX4439625.20_summits.bed INFO @ Sat, 15 Jan 2022 21:38:14: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (702 records, 4 fields): 3 millis CompletedMACS2peakCalling