Job ID = 12531652 SRX = SRX4555028 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8316004 spots for SRR7696723/SRR7696723.sra Written 8316004 spots for SRR7696723/SRR7696723.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: 00:09:56 8316004 reads; of these: 8316004 (100.00%) were paired; of these: 579460 (6.97%) aligned concordantly 0 times 4459673 (53.63%) aligned concordantly exactly 1 time 3276871 (39.40%) aligned concordantly >1 times ---- 579460 pairs aligned concordantly 0 times; of these: 34487 (5.95%) aligned discordantly 1 time ---- 544973 pairs aligned 0 times concordantly or discordantly; of these: 1089946 mates make up the pairs; of these: 901092 (82.67%) aligned 0 times 104237 (9.56%) aligned exactly 1 time 84617 (7.76%) aligned >1 times 94.58% overall alignment rate Time searching: 00:09:56 Overall time: 00:09:56 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 12 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] 1076606 / 3648644 = 0.2951 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 09:10:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.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 09:10:02: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:10:02: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:10:09: 1000000 INFO @ Sat, 17 Apr 2021 09:10:15: 2000000 INFO @ Sat, 17 Apr 2021 09:10:22: 3000000 INFO @ Sat, 17 Apr 2021 09:10:28: 4000000 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 09:10:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.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 09:10:32: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:10:32: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:10:34: 5000000 INFO @ Sat, 17 Apr 2021 09:10:39: 1000000 INFO @ Sat, 17 Apr 2021 09:10:41: 6000000 INFO @ Sat, 17 Apr 2021 09:10:46: 2000000 INFO @ Sat, 17 Apr 2021 09:10:47: 7000000 INFO @ Sat, 17 Apr 2021 09:10:52: 3000000 INFO @ Sat, 17 Apr 2021 09:10:53: 8000000 INFO @ Sat, 17 Apr 2021 09:10:59: 4000000 INFO @ Sat, 17 Apr 2021 09:10:59: 9000000 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 09:11:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.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 09:11:02: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:11:02: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:11:05: 10000000 INFO @ Sat, 17 Apr 2021 09:11:05: 5000000 INFO @ Sat, 17 Apr 2021 09:11:09: 1000000 INFO @ Sat, 17 Apr 2021 09:11:12: 11000000 INFO @ Sat, 17 Apr 2021 09:11:12: 6000000 INFO @ Sat, 17 Apr 2021 09:11:16: 2000000 INFO @ Sat, 17 Apr 2021 09:11:18: 7000000 INFO @ Sat, 17 Apr 2021 09:11:18: 12000000 INFO @ Sat, 17 Apr 2021 09:11:23: 3000000 INFO @ Sat, 17 Apr 2021 09:11:24: 8000000 INFO @ Sat, 17 Apr 2021 09:11:25: 13000000 INFO @ Sat, 17 Apr 2021 09:11:28: #1 tag size is determined as 99 bps INFO @ Sat, 17 Apr 2021 09:11:28: #1 tag size = 99 INFO @ Sat, 17 Apr 2021 09:11:28: #1 total tags in treatment: 6661411 INFO @ Sat, 17 Apr 2021 09:11:28: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:11:28: #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 09:11:29: #1 tags after filtering in treatment: 2049695 INFO @ Sat, 17 Apr 2021 09:11:29: #1 Redundant rate of treatment: 0.69 INFO @ Sat, 17 Apr 2021 09:11:29: #1 finished! INFO @ Sat, 17 Apr 2021 09:11:29: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:11:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:11:29: #2 number of paired peaks: 151 WARNING @ Sat, 17 Apr 2021 09:11:29: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Sat, 17 Apr 2021 09:11:29: start model_add_line... INFO @ Sat, 17 Apr 2021 09:11:29: start X-correlation... INFO @ Sat, 17 Apr 2021 09:11:29: end of X-cor INFO @ Sat, 17 Apr 2021 09:11:29: #2 finished! INFO @ Sat, 17 Apr 2021 09:11:29: #2 predicted fragment length is 4 bps INFO @ Sat, 17 Apr 2021 09:11:29: #2 alternative fragment length(s) may be 4,10,589 bps INFO @ Sat, 17 Apr 2021 09:11:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.05_model.r WARNING @ Sat, 17 Apr 2021 09:11:29: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:11:29: #2 You may need to consider one of the other alternative d(s): 4,10,589 WARNING @ Sat, 17 Apr 2021 09:11:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 09:11:29: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:11:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:11:30: 4000000 INFO @ Sat, 17 Apr 2021 09:11:30: 9000000 INFO @ Sat, 17 Apr 2021 09:11:33: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:11:34: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.05_peaks.xls INFO @ Sat, 17 Apr 2021 09:11:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:11:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.05_summits.bed INFO @ Sat, 17 Apr 2021 09:11:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:11:36: 10000000 INFO @ Sat, 17 Apr 2021 09:11:36: 5000000 INFO @ Sat, 17 Apr 2021 09:11:42: 11000000 INFO @ Sat, 17 Apr 2021 09:11:43: 6000000 INFO @ Sat, 17 Apr 2021 09:11:49: 12000000 INFO @ Sat, 17 Apr 2021 09:11:49: 7000000 INFO @ Sat, 17 Apr 2021 09:11:55: 8000000 INFO @ Sat, 17 Apr 2021 09:11:55: 13000000 INFO @ Sat, 17 Apr 2021 09:11:59: #1 tag size is determined as 99 bps INFO @ Sat, 17 Apr 2021 09:11:59: #1 tag size = 99 INFO @ Sat, 17 Apr 2021 09:11:59: #1 total tags in treatment: 6661411 INFO @ Sat, 17 Apr 2021 09:11:59: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:11:59: #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 09:11:59: #1 tags after filtering in treatment: 2049695 INFO @ Sat, 17 Apr 2021 09:11:59: #1 Redundant rate of treatment: 0.69 INFO @ Sat, 17 Apr 2021 09:11:59: #1 finished! INFO @ Sat, 17 Apr 2021 09:11:59: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:11:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:11:59: #2 number of paired peaks: 151 WARNING @ Sat, 17 Apr 2021 09:11:59: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Sat, 17 Apr 2021 09:11:59: start model_add_line... INFO @ Sat, 17 Apr 2021 09:11:59: start X-correlation... INFO @ Sat, 17 Apr 2021 09:11:59: end of X-cor INFO @ Sat, 17 Apr 2021 09:11:59: #2 finished! INFO @ Sat, 17 Apr 2021 09:11:59: #2 predicted fragment length is 4 bps INFO @ Sat, 17 Apr 2021 09:11:59: #2 alternative fragment length(s) may be 4,10,589 bps INFO @ Sat, 17 Apr 2021 09:11:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.10_model.r WARNING @ Sat, 17 Apr 2021 09:11:59: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:11:59: #2 You may need to consider one of the other alternative d(s): 4,10,589 WARNING @ Sat, 17 Apr 2021 09:11:59: #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 09:11:59: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:11:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:12:01: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 09:12:03: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:12:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.10_peaks.xls INFO @ Sat, 17 Apr 2021 09:12:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:12:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.10_summits.bed INFO @ Sat, 17 Apr 2021 09:12:05: Done! pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:12:07: 10000000 BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 09:12:14: 11000000 INFO @ Sat, 17 Apr 2021 09:12:20: 12000000 INFO @ Sat, 17 Apr 2021 09:12:26: 13000000 INFO @ Sat, 17 Apr 2021 09:12:30: #1 tag size is determined as 99 bps INFO @ Sat, 17 Apr 2021 09:12:30: #1 tag size = 99 INFO @ Sat, 17 Apr 2021 09:12:30: #1 total tags in treatment: 6661411 INFO @ Sat, 17 Apr 2021 09:12:30: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:12:30: #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 09:12:30: #1 tags after filtering in treatment: 2049695 INFO @ Sat, 17 Apr 2021 09:12:30: #1 Redundant rate of treatment: 0.69 INFO @ Sat, 17 Apr 2021 09:12:30: #1 finished! INFO @ Sat, 17 Apr 2021 09:12:30: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:12:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:12:30: #2 number of paired peaks: 151 WARNING @ Sat, 17 Apr 2021 09:12:30: Fewer paired peaks (151) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 151 pairs to build model! INFO @ Sat, 17 Apr 2021 09:12:30: start model_add_line... INFO @ Sat, 17 Apr 2021 09:12:30: start X-correlation... INFO @ Sat, 17 Apr 2021 09:12:30: end of X-cor INFO @ Sat, 17 Apr 2021 09:12:30: #2 finished! INFO @ Sat, 17 Apr 2021 09:12:30: #2 predicted fragment length is 4 bps INFO @ Sat, 17 Apr 2021 09:12:30: #2 alternative fragment length(s) may be 4,10,589 bps INFO @ Sat, 17 Apr 2021 09:12:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.20_model.r WARNING @ Sat, 17 Apr 2021 09:12:30: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:12:30: #2 You may need to consider one of the other alternative d(s): 4,10,589 WARNING @ Sat, 17 Apr 2021 09:12:30: #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 09:12:30: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:12:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:12:34: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:12:36: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.20_peaks.xls INFO @ Sat, 17 Apr 2021 09:12:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:12:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX4555028/SRX4555028.20_summits.bed INFO @ Sat, 17 Apr 2021 09:12:36: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling