Job ID = 12531632 SRX = SRX4555013 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5697042 spots for SRR7696703/SRR7696703.sra Written 5697042 spots for SRR7696703/SRR7696703.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: 00:06:28 5697042 reads; of these: 5697042 (100.00%) were paired; of these: 282465 (4.96%) aligned concordantly 0 times 2135018 (37.48%) aligned concordantly exactly 1 time 3279559 (57.57%) aligned concordantly >1 times ---- 282465 pairs aligned concordantly 0 times; of these: 19883 (7.04%) aligned discordantly 1 time ---- 262582 pairs aligned 0 times concordantly or discordantly; of these: 525164 mates make up the pairs; of these: 374769 (71.36%) aligned 0 times 69337 (13.20%) aligned exactly 1 time 81058 (15.43%) aligned >1 times 96.71% overall alignment rate Time searching: 00:06:28 Overall time: 00:06:28 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_sort_core] merging from 8 files... [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] 1160790 / 2455913 = 0.4727 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 08:55:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.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, 17 Apr 2021 08:55:19: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:55:19: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:55:26: 1000000 INFO @ Sat, 17 Apr 2021 08:55:33: 2000000 INFO @ Sat, 17 Apr 2021 08:55:40: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 08:55:47: 4000000 INFO @ Sat, 17 Apr 2021 08:55:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.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, 17 Apr 2021 08:55:49: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:55:49: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:55:54: 5000000 INFO @ Sat, 17 Apr 2021 08:55:56: 1000000 INFO @ Sat, 17 Apr 2021 08:56:01: 6000000 INFO @ Sat, 17 Apr 2021 08:56:04: 2000000 INFO @ Sat, 17 Apr 2021 08:56:08: 7000000 INFO @ Sat, 17 Apr 2021 08:56:11: 3000000 INFO @ Sat, 17 Apr 2021 08:56:15: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 08:56:18: 4000000 INFO @ Sat, 17 Apr 2021 08:56:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.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, 17 Apr 2021 08:56:19: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:56:19: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:56:20: #1 tag size is determined as 123 bps INFO @ Sat, 17 Apr 2021 08:56:20: #1 tag size = 123 INFO @ Sat, 17 Apr 2021 08:56:20: #1 total tags in treatment: 4255447 INFO @ Sat, 17 Apr 2021 08:56:20: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:56:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 08:56:20: #1 tags after filtering in treatment: 1202698 INFO @ Sat, 17 Apr 2021 08:56:20: #1 Redundant rate of treatment: 0.72 INFO @ Sat, 17 Apr 2021 08:56:20: #1 finished! INFO @ Sat, 17 Apr 2021 08:56:20: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:56:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:56:21: #2 number of paired peaks: 193 WARNING @ Sat, 17 Apr 2021 08:56:21: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 17 Apr 2021 08:56:21: start model_add_line... INFO @ Sat, 17 Apr 2021 08:56:21: start X-correlation... INFO @ Sat, 17 Apr 2021 08:56:21: end of X-cor INFO @ Sat, 17 Apr 2021 08:56:21: #2 finished! INFO @ Sat, 17 Apr 2021 08:56:21: #2 predicted fragment length is 52 bps INFO @ Sat, 17 Apr 2021 08:56:21: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sat, 17 Apr 2021 08:56:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.05_model.r WARNING @ Sat, 17 Apr 2021 08:56:21: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:56:21: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sat, 17 Apr 2021 08:56:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:56:21: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:56:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:56:24: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:56:25: 5000000 INFO @ Sat, 17 Apr 2021 08:56:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.05_peaks.xls INFO @ Sat, 17 Apr 2021 08:56:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:56:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.05_summits.bed INFO @ Sat, 17 Apr 2021 08:56:25: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1393 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:56:26: 1000000 INFO @ Sat, 17 Apr 2021 08:56:32: 6000000 INFO @ Sat, 17 Apr 2021 08:56:34: 2000000 INFO @ Sat, 17 Apr 2021 08:56:39: 7000000 INFO @ Sat, 17 Apr 2021 08:56:41: 3000000 INFO @ Sat, 17 Apr 2021 08:56:46: 8000000 INFO @ Sat, 17 Apr 2021 08:56:48: 4000000 INFO @ Sat, 17 Apr 2021 08:56:51: #1 tag size is determined as 123 bps INFO @ Sat, 17 Apr 2021 08:56:51: #1 tag size = 123 INFO @ Sat, 17 Apr 2021 08:56:51: #1 total tags in treatment: 4255447 INFO @ Sat, 17 Apr 2021 08:56:51: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:56:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 08:56:51: #1 tags after filtering in treatment: 1202698 INFO @ Sat, 17 Apr 2021 08:56:51: #1 Redundant rate of treatment: 0.72 INFO @ Sat, 17 Apr 2021 08:56:51: #1 finished! INFO @ Sat, 17 Apr 2021 08:56:51: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:56:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:56:51: #2 number of paired peaks: 193 WARNING @ Sat, 17 Apr 2021 08:56:51: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 17 Apr 2021 08:56:51: start model_add_line... INFO @ Sat, 17 Apr 2021 08:56:51: start X-correlation... INFO @ Sat, 17 Apr 2021 08:56:52: end of X-cor INFO @ Sat, 17 Apr 2021 08:56:52: #2 finished! INFO @ Sat, 17 Apr 2021 08:56:52: #2 predicted fragment length is 52 bps INFO @ Sat, 17 Apr 2021 08:56:52: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sat, 17 Apr 2021 08:56:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.10_model.r WARNING @ Sat, 17 Apr 2021 08:56:52: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:56:52: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sat, 17 Apr 2021 08:56:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:56:52: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:56:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:56:54: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:56:55: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 08:56:56: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.10_peaks.xls INFO @ Sat, 17 Apr 2021 08:56:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:56:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.10_summits.bed INFO @ Sat, 17 Apr 2021 08:56:56: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (696 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 08:57:02: 6000000 INFO @ Sat, 17 Apr 2021 08:57:09: 7000000 INFO @ Sat, 17 Apr 2021 08:57:15: 8000000 INFO @ Sat, 17 Apr 2021 08:57:21: #1 tag size is determined as 123 bps INFO @ Sat, 17 Apr 2021 08:57:21: #1 tag size = 123 INFO @ Sat, 17 Apr 2021 08:57:21: #1 total tags in treatment: 4255447 INFO @ Sat, 17 Apr 2021 08:57:21: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:57:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 08:57:21: #1 tags after filtering in treatment: 1202698 INFO @ Sat, 17 Apr 2021 08:57:21: #1 Redundant rate of treatment: 0.72 INFO @ Sat, 17 Apr 2021 08:57:21: #1 finished! INFO @ Sat, 17 Apr 2021 08:57:21: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:57:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:57:21: #2 number of paired peaks: 193 WARNING @ Sat, 17 Apr 2021 08:57:21: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 17 Apr 2021 08:57:21: start model_add_line... INFO @ Sat, 17 Apr 2021 08:57:21: start X-correlation... INFO @ Sat, 17 Apr 2021 08:57:21: end of X-cor INFO @ Sat, 17 Apr 2021 08:57:21: #2 finished! INFO @ Sat, 17 Apr 2021 08:57:21: #2 predicted fragment length is 52 bps INFO @ Sat, 17 Apr 2021 08:57:21: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sat, 17 Apr 2021 08:57:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.20_model.r WARNING @ Sat, 17 Apr 2021 08:57:21: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:57:21: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sat, 17 Apr 2021 08:57:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:57:21: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:57:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:57:24: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:57:25: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.20_peaks.xls INFO @ Sat, 17 Apr 2021 08:57:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:57:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555013/SRX4555013.20_summits.bed INFO @ Sat, 17 Apr 2021 08:57:25: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (146 records, 4 fields): 2 millis CompletedMACS2peakCalling