Job ID = 14521742 SRX = ERX4439632 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3475912 spots for ERR4501561/ERR4501561.sra Written 3475912 spots for ERR4501561/ERR4501561.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: 00:04:19 3475912 reads; of these: 3475912 (100.00%) were paired; of these: 734516 (21.13%) aligned concordantly 0 times 2422091 (69.68%) aligned concordantly exactly 1 time 319305 (9.19%) aligned concordantly >1 times ---- 734516 pairs aligned concordantly 0 times; of these: 381959 (52.00%) aligned discordantly 1 time ---- 352557 pairs aligned 0 times concordantly or discordantly; of these: 705114 mates make up the pairs; of these: 546049 (77.44%) aligned 0 times 53652 (7.61%) aligned exactly 1 time 105413 (14.95%) aligned >1 times 92.15% overall alignment rate Time searching: 00:04:19 Overall time: 00:04:19 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] 98178 / 3096306 = 0.0317 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 21:41:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.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 21:41:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:41:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:41:09: 1000000 INFO @ Sat, 15 Jan 2022 21:41:16: 2000000 INFO @ Sat, 15 Jan 2022 21:41:23: 3000000 INFO @ Sat, 15 Jan 2022 21:41:30: 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 21:41:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.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 21:41:32: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:41:32: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:41:37: 5000000 INFO @ Sat, 15 Jan 2022 21:41:39: 1000000 INFO @ Sat, 15 Jan 2022 21:41:44: 6000000 INFO @ Sat, 15 Jan 2022 21:41:45: 2000000 INFO @ Sat, 15 Jan 2022 21:41:45: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:41:45: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:41:45: #1 total tags in treatment: 2665739 INFO @ Sat, 15 Jan 2022 21:41:45: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:41:45: #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 21:41:45: #1 tags after filtering in treatment: 1942093 INFO @ Sat, 15 Jan 2022 21:41:45: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:41:45: #1 finished! INFO @ Sat, 15 Jan 2022 21:41:45: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:41:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:41:45: #2 number of paired peaks: 254 WARNING @ Sat, 15 Jan 2022 21:41:45: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Sat, 15 Jan 2022 21:41:45: start model_add_line... INFO @ Sat, 15 Jan 2022 21:41:45: start X-correlation... INFO @ Sat, 15 Jan 2022 21:41:45: end of X-cor INFO @ Sat, 15 Jan 2022 21:41:45: #2 finished! INFO @ Sat, 15 Jan 2022 21:41:45: #2 predicted fragment length is 180 bps INFO @ Sat, 15 Jan 2022 21:41:45: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 15 Jan 2022 21:41:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.05_model.r WARNING @ Sat, 15 Jan 2022 21:41:45: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:41:45: #2 You may need to consider one of the other alternative d(s): 180 WARNING @ Sat, 15 Jan 2022 21:41:45: #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 21:41:45: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:41:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:41:51: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:41:51: 3000000 INFO @ Sat, 15 Jan 2022 21:41:52: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:41:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:41:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.05_summits.bed INFO @ Sat, 15 Jan 2022 21:41:52: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1559 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:41:57: 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 21:42:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.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 21:42:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:42:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:42:03: 5000000 INFO @ Sat, 15 Jan 2022 21:42:09: 6000000 INFO @ Sat, 15 Jan 2022 21:42:10: 1000000 INFO @ Sat, 15 Jan 2022 21:42:10: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:42:10: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:42:10: #1 total tags in treatment: 2665739 INFO @ Sat, 15 Jan 2022 21:42:10: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:42:10: #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 21:42:10: #1 tags after filtering in treatment: 1942093 INFO @ Sat, 15 Jan 2022 21:42:10: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:42:10: #1 finished! INFO @ Sat, 15 Jan 2022 21:42:10: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:42:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:42:11: #2 number of paired peaks: 254 WARNING @ Sat, 15 Jan 2022 21:42:11: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Sat, 15 Jan 2022 21:42:11: start model_add_line... INFO @ Sat, 15 Jan 2022 21:42:11: start X-correlation... INFO @ Sat, 15 Jan 2022 21:42:11: end of X-cor INFO @ Sat, 15 Jan 2022 21:42:11: #2 finished! INFO @ Sat, 15 Jan 2022 21:42:11: #2 predicted fragment length is 180 bps INFO @ Sat, 15 Jan 2022 21:42:11: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 15 Jan 2022 21:42:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.10_model.r WARNING @ Sat, 15 Jan 2022 21:42:11: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:42:11: #2 You may need to consider one of the other alternative d(s): 180 WARNING @ Sat, 15 Jan 2022 21:42:11: #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 21:42:11: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:42:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:42:16: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:42:17: 2000000 INFO @ Sat, 15 Jan 2022 21:42:18: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:42:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:42:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.10_summits.bed INFO @ Sat, 15 Jan 2022 21:42:18: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1193 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:42:24: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:42:31: 4000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:42:38: 5000000 INFO @ Sat, 15 Jan 2022 21:42:45: 6000000 INFO @ Sat, 15 Jan 2022 21:42:47: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:42:47: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:42:47: #1 total tags in treatment: 2665739 INFO @ Sat, 15 Jan 2022 21:42:47: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:42:47: #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 21:42:47: #1 tags after filtering in treatment: 1942093 INFO @ Sat, 15 Jan 2022 21:42:47: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 15 Jan 2022 21:42:47: #1 finished! INFO @ Sat, 15 Jan 2022 21:42:47: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:42:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:42:47: #2 number of paired peaks: 254 WARNING @ Sat, 15 Jan 2022 21:42:47: Fewer paired peaks (254) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 254 pairs to build model! INFO @ Sat, 15 Jan 2022 21:42:47: start model_add_line... INFO @ Sat, 15 Jan 2022 21:42:47: start X-correlation... INFO @ Sat, 15 Jan 2022 21:42:47: end of X-cor INFO @ Sat, 15 Jan 2022 21:42:47: #2 finished! INFO @ Sat, 15 Jan 2022 21:42:47: #2 predicted fragment length is 180 bps INFO @ Sat, 15 Jan 2022 21:42:47: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 15 Jan 2022 21:42:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.20_model.r WARNING @ Sat, 15 Jan 2022 21:42:47: #2 Since the d (180) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:42:47: #2 You may need to consider one of the other alternative d(s): 180 WARNING @ Sat, 15 Jan 2022 21:42:47: #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 21:42:47: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:42:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:42:53: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:42:55: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:42:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:42:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439632/ERX4439632.20_summits.bed INFO @ Sat, 15 Jan 2022 21:42:55: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (882 records, 4 fields): 3 millis CompletedMACS2peakCalling