Job ID = 14521227 SRX = SRX8245382 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 6474207 spots for SRR11684593/SRR11684593.sra Written 6474207 spots for SRR11684593/SRR11684593.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 6474207 reads; of these: 6474207 (100.00%) were paired; of these: 3552691 (54.87%) aligned concordantly 0 times 2706304 (41.80%) aligned concordantly exactly 1 time 215212 (3.32%) aligned concordantly >1 times ---- 3552691 pairs aligned concordantly 0 times; of these: 8740 (0.25%) aligned discordantly 1 time ---- 3543951 pairs aligned 0 times concordantly or discordantly; of these: 7087902 mates make up the pairs; of these: 4452477 (62.82%) aligned 0 times 2374738 (33.50%) aligned exactly 1 time 260687 (3.68%) aligned >1 times 65.61% 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] 158777 / 2929369 = 0.0542 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 20:46:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.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 20:46:17: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:46:17: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:46:22: 1000000 INFO @ Sat, 15 Jan 2022 20:46:27: 2000000 INFO @ Sat, 15 Jan 2022 20:46:31: 3000000 INFO @ Sat, 15 Jan 2022 20:46:36: 4000000 INFO @ Sat, 15 Jan 2022 20:46:40: 5000000 INFO @ Sat, 15 Jan 2022 20:46:45: 6000000 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 20:46:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.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 20:46:47: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:46:47: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:46:50: 7000000 INFO @ Sat, 15 Jan 2022 20:46:52: 1000000 INFO @ Sat, 15 Jan 2022 20:46:55: 8000000 INFO @ Sat, 15 Jan 2022 20:46:56: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:46:56: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:46:56: #1 total tags in treatment: 2763464 INFO @ Sat, 15 Jan 2022 20:46:56: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:46:56: #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 20:46:56: #1 tags after filtering in treatment: 1429318 INFO @ Sat, 15 Jan 2022 20:46:56: #1 Redundant rate of treatment: 0.48 INFO @ Sat, 15 Jan 2022 20:46:56: #1 finished! INFO @ Sat, 15 Jan 2022 20:46:56: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:46:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:46:56: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:46:56: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Jan 2022 20:46:56: start model_add_line... INFO @ Sat, 15 Jan 2022 20:46:56: start X-correlation... INFO @ Sat, 15 Jan 2022 20:46:56: end of X-cor INFO @ Sat, 15 Jan 2022 20:46:56: #2 finished! INFO @ Sat, 15 Jan 2022 20:46:56: #2 predicted fragment length is 63 bps INFO @ Sat, 15 Jan 2022 20:46:56: #2 alternative fragment length(s) may be 28,42,63,87,94,97,124,134,176,199,210,215,247,276,310,322,389,403,480,501,520,525,561,579 bps INFO @ Sat, 15 Jan 2022 20:46:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.05_model.r WARNING @ Sat, 15 Jan 2022 20:46:56: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:46:56: #2 You may need to consider one of the other alternative d(s): 28,42,63,87,94,97,124,134,176,199,210,215,247,276,310,322,389,403,480,501,520,525,561,579 WARNING @ Sat, 15 Jan 2022 20:46:56: #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 20:46:56: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:46:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:46:57: 2000000 INFO @ Sat, 15 Jan 2022 20:46:58: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:47:00: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.05_peaks.xls INFO @ Sat, 15 Jan 2022 20:47:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:47:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.05_summits.bed INFO @ Sat, 15 Jan 2022 20:47:00: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (85 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:47:02: 3000000 INFO @ Sat, 15 Jan 2022 20:47:07: 4000000 INFO @ Sat, 15 Jan 2022 20:47:11: 5000000 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 20:47:16: 6000000 INFO @ Sat, 15 Jan 2022 20:47:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.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 20:47:17: #1 read tag files... INFO @ Sat, 15 Jan 2022 20:47:17: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 20:47:21: 7000000 INFO @ Sat, 15 Jan 2022 20:47:23: 1000000 INFO @ Sat, 15 Jan 2022 20:47:27: 8000000 INFO @ Sat, 15 Jan 2022 20:47:27: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:47:27: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:47:27: #1 total tags in treatment: 2763464 INFO @ Sat, 15 Jan 2022 20:47:27: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:47:27: #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 20:47:28: #1 tags after filtering in treatment: 1429318 INFO @ Sat, 15 Jan 2022 20:47:28: #1 Redundant rate of treatment: 0.48 INFO @ Sat, 15 Jan 2022 20:47:28: #1 finished! INFO @ Sat, 15 Jan 2022 20:47:28: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:47:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:47:28: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:47:28: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Jan 2022 20:47:28: start model_add_line... INFO @ Sat, 15 Jan 2022 20:47:28: start X-correlation... INFO @ Sat, 15 Jan 2022 20:47:28: end of X-cor INFO @ Sat, 15 Jan 2022 20:47:28: #2 finished! INFO @ Sat, 15 Jan 2022 20:47:28: #2 predicted fragment length is 63 bps INFO @ Sat, 15 Jan 2022 20:47:28: #2 alternative fragment length(s) may be 28,42,63,87,94,97,124,134,176,199,210,215,247,276,310,322,389,403,480,501,520,525,561,579 bps INFO @ Sat, 15 Jan 2022 20:47:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.10_model.r WARNING @ Sat, 15 Jan 2022 20:47:28: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:47:28: #2 You may need to consider one of the other alternative d(s): 28,42,63,87,94,97,124,134,176,199,210,215,247,276,310,322,389,403,480,501,520,525,561,579 WARNING @ Sat, 15 Jan 2022 20:47:28: #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 20:47:28: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:47:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:47:29: 2000000 INFO @ Sat, 15 Jan 2022 20:47:30: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:47:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.10_peaks.xls INFO @ Sat, 15 Jan 2022 20:47:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:47:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.10_summits.bed INFO @ Sat, 15 Jan 2022 20:47:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 20:47:35: 3000000 INFO @ Sat, 15 Jan 2022 20:47:40: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 20:47:46: 5000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 20:47:51: 6000000 INFO @ Sat, 15 Jan 2022 20:47:57: 7000000 INFO @ Sat, 15 Jan 2022 20:48:03: 8000000 INFO @ Sat, 15 Jan 2022 20:48:04: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 20:48:06: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 20:48:06: #1 total tags in treatment: 2763464 INFO @ Sat, 15 Jan 2022 20:48:06: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 20:48:06: #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 20:48:06: #1 tags after filtering in treatment: 1429318 INFO @ Sat, 15 Jan 2022 20:48:06: #1 Redundant rate of treatment: 0.48 INFO @ Sat, 15 Jan 2022 20:48:06: #1 finished! INFO @ Sat, 15 Jan 2022 20:48:06: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 20:48:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 20:48:06: #2 number of paired peaks: 173 WARNING @ Sat, 15 Jan 2022 20:48:06: Fewer paired peaks (173) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 173 pairs to build model! INFO @ Sat, 15 Jan 2022 20:48:06: start model_add_line... INFO @ Sat, 15 Jan 2022 20:48:06: start X-correlation... INFO @ Sat, 15 Jan 2022 20:48:06: end of X-cor INFO @ Sat, 15 Jan 2022 20:48:06: #2 finished! INFO @ Sat, 15 Jan 2022 20:48:06: #2 predicted fragment length is 63 bps INFO @ Sat, 15 Jan 2022 20:48:06: #2 alternative fragment length(s) may be 28,42,63,87,94,97,124,134,176,199,210,215,247,276,310,322,389,403,480,501,520,525,561,579 bps INFO @ Sat, 15 Jan 2022 20:48:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.20_model.r WARNING @ Sat, 15 Jan 2022 20:48:06: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 20:48:06: #2 You may need to consider one of the other alternative d(s): 28,42,63,87,94,97,124,134,176,199,210,215,247,276,310,322,389,403,480,501,520,525,561,579 WARNING @ Sat, 15 Jan 2022 20:48:06: #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 20:48:06: #3 Call peaks... INFO @ Sat, 15 Jan 2022 20:48:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 20:48:08: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 20:48:09: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.20_peaks.xls INFO @ Sat, 15 Jan 2022 20:48:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 20:48:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8245382/SRX8245382.20_summits.bed INFO @ Sat, 15 Jan 2022 20:48:09: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (4 records, 4 fields): 1 millis CompletedMACS2peakCalling