Job ID = 14521688 SRX = ERX4439618 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3316389 spots for ERR4501547/ERR4501547.sra Written 3316389 spots for ERR4501547/ERR4501547.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: 00:03:48 3316389 reads; of these: 3316389 (100.00%) were paired; of these: 925812 (27.92%) aligned concordantly 0 times 2014390 (60.74%) aligned concordantly exactly 1 time 376187 (11.34%) aligned concordantly >1 times ---- 925812 pairs aligned concordantly 0 times; of these: 355143 (38.36%) aligned discordantly 1 time ---- 570669 pairs aligned 0 times concordantly or discordantly; of these: 1141338 mates make up the pairs; of these: 937397 (82.13%) aligned 0 times 52175 (4.57%) aligned exactly 1 time 151766 (13.30%) aligned >1 times 85.87% overall alignment rate Time searching: 00:03:48 Overall time: 00:03:48 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] 49879 / 2719091 = 0.0183 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 21:33:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.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 21:33:06: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:33:06: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:33:16: 1000000 INFO @ Sat, 15 Jan 2022 21:33:27: 2000000 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 21:33:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.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 21:33:36: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:33:36: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:33:38: 3000000 INFO @ Sat, 15 Jan 2022 21:33:48: 1000000 INFO @ Sat, 15 Jan 2022 21:33:48: 4000000 INFO @ Sat, 15 Jan 2022 21:33:59: 5000000 INFO @ Sat, 15 Jan 2022 21:34:00: 2000000 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 21:34:05: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:34:05: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:34:05: #1 total tags in treatment: 2347311 INFO @ Sat, 15 Jan 2022 21:34:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:34:05: #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 21:34:05: #1 tags after filtering in treatment: 2019711 INFO @ Sat, 15 Jan 2022 21:34:05: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Jan 2022 21:34:05: #1 finished! INFO @ Sat, 15 Jan 2022 21:34:05: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:34:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:34:05: #2 number of paired peaks: 166 WARNING @ Sat, 15 Jan 2022 21:34:05: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Sat, 15 Jan 2022 21:34:05: start model_add_line... INFO @ Sat, 15 Jan 2022 21:34:05: start X-correlation... INFO @ Sat, 15 Jan 2022 21:34:05: end of X-cor INFO @ Sat, 15 Jan 2022 21:34:05: #2 finished! INFO @ Sat, 15 Jan 2022 21:34:05: #2 predicted fragment length is 147 bps INFO @ Sat, 15 Jan 2022 21:34:05: #2 alternative fragment length(s) may be 1,134,147,549,589,596 bps INFO @ Sat, 15 Jan 2022 21:34:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.05_model.r WARNING @ Sat, 15 Jan 2022 21:34:05: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:34:05: #2 You may need to consider one of the other alternative d(s): 1,134,147,549,589,596 WARNING @ Sat, 15 Jan 2022 21:34:05: #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 21:34:05: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:34:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:34:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.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 21:34:06: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:34:06: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:34:10: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:34:12: 3000000 INFO @ Sat, 15 Jan 2022 21:34:12: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:34:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:34:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.05_summits.bed INFO @ Sat, 15 Jan 2022 21:34:12: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (48 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:34:17: 1000000 INFO @ Sat, 15 Jan 2022 21:34:24: 4000000 INFO @ Sat, 15 Jan 2022 21:34:28: 2000000 INFO @ Sat, 15 Jan 2022 21:34:35: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:34:39: 3000000 INFO @ Sat, 15 Jan 2022 21:34:41: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:34:41: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:34:41: #1 total tags in treatment: 2347311 INFO @ Sat, 15 Jan 2022 21:34:41: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:34:41: #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 21:34:41: #1 tags after filtering in treatment: 2019711 INFO @ Sat, 15 Jan 2022 21:34:41: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Jan 2022 21:34:41: #1 finished! INFO @ Sat, 15 Jan 2022 21:34:41: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:34:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:34:41: #2 number of paired peaks: 166 WARNING @ Sat, 15 Jan 2022 21:34:41: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Sat, 15 Jan 2022 21:34:41: start model_add_line... INFO @ Sat, 15 Jan 2022 21:34:41: start X-correlation... INFO @ Sat, 15 Jan 2022 21:34:41: end of X-cor INFO @ Sat, 15 Jan 2022 21:34:41: #2 finished! INFO @ Sat, 15 Jan 2022 21:34:41: #2 predicted fragment length is 147 bps INFO @ Sat, 15 Jan 2022 21:34:41: #2 alternative fragment length(s) may be 1,134,147,549,589,596 bps INFO @ Sat, 15 Jan 2022 21:34:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.10_model.r WARNING @ Sat, 15 Jan 2022 21:34:41: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:34:41: #2 You may need to consider one of the other alternative d(s): 1,134,147,549,589,596 WARNING @ Sat, 15 Jan 2022 21:34:41: #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 21:34:41: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:34:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:34:46: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:34:48: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:34:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:34:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.10_summits.bed INFO @ Sat, 15 Jan 2022 21:34:48: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (14 records, 4 fields): 24 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:34:51: 4000000 INFO @ Sat, 15 Jan 2022 21:35:02: 5000000 INFO @ Sat, 15 Jan 2022 21:35:09: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:35:09: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:35:09: #1 total tags in treatment: 2347311 INFO @ Sat, 15 Jan 2022 21:35:09: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:35:09: #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 21:35:09: #1 tags after filtering in treatment: 2019711 INFO @ Sat, 15 Jan 2022 21:35:09: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Jan 2022 21:35:09: #1 finished! INFO @ Sat, 15 Jan 2022 21:35:09: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:35:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:35:09: #2 number of paired peaks: 166 WARNING @ Sat, 15 Jan 2022 21:35:09: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Sat, 15 Jan 2022 21:35:09: start model_add_line... INFO @ Sat, 15 Jan 2022 21:35:09: start X-correlation... INFO @ Sat, 15 Jan 2022 21:35:09: end of X-cor INFO @ Sat, 15 Jan 2022 21:35:09: #2 finished! INFO @ Sat, 15 Jan 2022 21:35:09: #2 predicted fragment length is 147 bps INFO @ Sat, 15 Jan 2022 21:35:09: #2 alternative fragment length(s) may be 1,134,147,549,589,596 bps INFO @ Sat, 15 Jan 2022 21:35:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.20_model.r WARNING @ Sat, 15 Jan 2022 21:35:10: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:35:10: #2 You may need to consider one of the other alternative d(s): 1,134,147,549,589,596 WARNING @ Sat, 15 Jan 2022 21:35:10: #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 21:35:10: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:35:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:35:14: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:35:16: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:35:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:35:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439618/ERX4439618.20_summits.bed INFO @ Sat, 15 Jan 2022 21:35:16: Done! pass1 - making usageList (1 chroms): 0 millis pass2 - checking and writing primary data (1 records, 4 fields): 129 millis CompletedMACS2peakCalling