Job ID = 14521907 SRX = ERX4439588 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 3839488 spots for ERR4501517/ERR4501517.sra Written 3839488 spots for ERR4501517/ERR4501517.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: 00:03:00 3839488 reads; of these: 3839488 (100.00%) were paired; of these: 1031844 (26.87%) aligned concordantly 0 times 2402218 (62.57%) aligned concordantly exactly 1 time 405426 (10.56%) aligned concordantly >1 times ---- 1031844 pairs aligned concordantly 0 times; of these: 454099 (44.01%) aligned discordantly 1 time ---- 577745 pairs aligned 0 times concordantly or discordantly; of these: 1155490 mates make up the pairs; of these: 927081 (80.23%) aligned 0 times 63449 (5.49%) aligned exactly 1 time 164960 (14.28%) aligned >1 times 87.93% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 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] 56496 / 3230335 = 0.0175 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 21:56:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.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 21:56:52: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:56:52: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:56:58: 1000000 INFO @ Sat, 15 Jan 2022 21:57:03: 2000000 INFO @ Sat, 15 Jan 2022 21:57:08: 3000000 INFO @ Sat, 15 Jan 2022 21:57:14: 4000000 INFO @ Sat, 15 Jan 2022 21:57:19: 5000000 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 21:57:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.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 21:57:22: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:57:22: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:57:25: 6000000 INFO @ Sat, 15 Jan 2022 21:57:28: 1000000 INFO @ Sat, 15 Jan 2022 21:57:29: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:57:29: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:57:29: #1 total tags in treatment: 2759402 INFO @ Sat, 15 Jan 2022 21:57:29: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:57:29: #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 21:57:29: #1 tags after filtering in treatment: 2387698 INFO @ Sat, 15 Jan 2022 21:57:29: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Jan 2022 21:57:29: #1 finished! INFO @ Sat, 15 Jan 2022 21:57:29: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:57:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:57:29: #2 number of paired peaks: 106 WARNING @ Sat, 15 Jan 2022 21:57:29: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Sat, 15 Jan 2022 21:57:29: start model_add_line... INFO @ Sat, 15 Jan 2022 21:57:29: start X-correlation... INFO @ Sat, 15 Jan 2022 21:57:29: end of X-cor INFO @ Sat, 15 Jan 2022 21:57:29: #2 finished! INFO @ Sat, 15 Jan 2022 21:57:29: #2 predicted fragment length is 165 bps INFO @ Sat, 15 Jan 2022 21:57:29: #2 alternative fragment length(s) may be 1,131,165,575,580 bps INFO @ Sat, 15 Jan 2022 21:57:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.05_model.r WARNING @ Sat, 15 Jan 2022 21:57:29: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:57:29: #2 You may need to consider one of the other alternative d(s): 1,131,165,575,580 WARNING @ Sat, 15 Jan 2022 21:57:29: #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 21:57:29: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:57:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:57:33: 2000000 INFO @ Sat, 15 Jan 2022 21:57:33: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:57:35: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.05_peaks.xls INFO @ Sat, 15 Jan 2022 21:57:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:57:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.05_summits.bed INFO @ Sat, 15 Jan 2022 21:57:35: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (41 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:57:39: 3000000 INFO @ Sat, 15 Jan 2022 21:57:45: 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 21:57:50: 5000000 INFO @ Sat, 15 Jan 2022 21:57:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.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 21:57:52: #1 read tag files... INFO @ Sat, 15 Jan 2022 21:57:52: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 21:57:56: 6000000 INFO @ Sat, 15 Jan 2022 21:57:58: 1000000 INFO @ Sat, 15 Jan 2022 21:58:00: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:58:00: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:58:00: #1 total tags in treatment: 2759402 INFO @ Sat, 15 Jan 2022 21:58:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:58:00: #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 21:58:00: #1 tags after filtering in treatment: 2387698 INFO @ Sat, 15 Jan 2022 21:58:00: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Jan 2022 21:58:00: #1 finished! INFO @ Sat, 15 Jan 2022 21:58:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:58:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:58:00: #2 number of paired peaks: 106 WARNING @ Sat, 15 Jan 2022 21:58:00: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Sat, 15 Jan 2022 21:58:00: start model_add_line... INFO @ Sat, 15 Jan 2022 21:58:00: start X-correlation... INFO @ Sat, 15 Jan 2022 21:58:00: end of X-cor INFO @ Sat, 15 Jan 2022 21:58:00: #2 finished! INFO @ Sat, 15 Jan 2022 21:58:00: #2 predicted fragment length is 165 bps INFO @ Sat, 15 Jan 2022 21:58:00: #2 alternative fragment length(s) may be 1,131,165,575,580 bps INFO @ Sat, 15 Jan 2022 21:58:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.10_model.r WARNING @ Sat, 15 Jan 2022 21:58:00: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:58:00: #2 You may need to consider one of the other alternative d(s): 1,131,165,575,580 WARNING @ Sat, 15 Jan 2022 21:58:00: #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 21:58:00: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:58:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:58:04: 2000000 INFO @ Sat, 15 Jan 2022 21:58:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:58:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.10_peaks.xls INFO @ Sat, 15 Jan 2022 21:58:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:58:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.10_summits.bed INFO @ Sat, 15 Jan 2022 21:58:07: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (12 records, 4 fields): 155 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 21:58:09: 3000000 INFO @ Sat, 15 Jan 2022 21:58:15: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 21:58:21: 5000000 INFO @ Sat, 15 Jan 2022 21:58:27: 6000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 21:58:31: #1 tag size is determined as 100 bps INFO @ Sat, 15 Jan 2022 21:58:31: #1 tag size = 100 INFO @ Sat, 15 Jan 2022 21:58:31: #1 total tags in treatment: 2759402 INFO @ Sat, 15 Jan 2022 21:58:31: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 21:58:31: #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 21:58:31: #1 tags after filtering in treatment: 2387698 INFO @ Sat, 15 Jan 2022 21:58:31: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 15 Jan 2022 21:58:31: #1 finished! INFO @ Sat, 15 Jan 2022 21:58:31: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 21:58:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 21:58:31: #2 number of paired peaks: 106 WARNING @ Sat, 15 Jan 2022 21:58:31: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Sat, 15 Jan 2022 21:58:31: start model_add_line... INFO @ Sat, 15 Jan 2022 21:58:31: start X-correlation... INFO @ Sat, 15 Jan 2022 21:58:31: end of X-cor INFO @ Sat, 15 Jan 2022 21:58:31: #2 finished! INFO @ Sat, 15 Jan 2022 21:58:31: #2 predicted fragment length is 165 bps INFO @ Sat, 15 Jan 2022 21:58:31: #2 alternative fragment length(s) may be 1,131,165,575,580 bps INFO @ Sat, 15 Jan 2022 21:58:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.20_model.r WARNING @ Sat, 15 Jan 2022 21:58:31: #2 Since the d (165) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 21:58:31: #2 You may need to consider one of the other alternative d(s): 1,131,165,575,580 WARNING @ Sat, 15 Jan 2022 21:58:31: #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 21:58:31: #3 Call peaks... INFO @ Sat, 15 Jan 2022 21:58:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 21:58:35: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 21:58:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.20_peaks.xls INFO @ Sat, 15 Jan 2022 21:58:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 21:58:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX4439588/ERX4439588.20_summits.bed INFO @ Sat, 15 Jan 2022 21:58:37: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 0 millis CompletedMACS2peakCalling