Job ID = 14520221 SRX = SRX8398411 Genome = sacCer3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 2193269 spots for SRR11848053/SRR11848053.sra Written 2193269 spots for SRR11848053/SRR11848053.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: 00:01:22 2193269 reads; of these: 2193269 (100.00%) were paired; of these: 419566 (19.13%) aligned concordantly 0 times 1558433 (71.06%) aligned concordantly exactly 1 time 215270 (9.82%) aligned concordantly >1 times ---- 419566 pairs aligned concordantly 0 times; of these: 56538 (13.48%) aligned discordantly 1 time ---- 363028 pairs aligned 0 times concordantly or discordantly; of these: 726056 mates make up the pairs; of these: 689750 (95.00%) aligned 0 times 21667 (2.98%) aligned exactly 1 time 14639 (2.02%) aligned >1 times 84.28% overall alignment rate Time searching: 00:01:22 Overall time: 00:01:22 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] 119143 / 1806950 = 0.0659 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 18:44:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.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 18:44:27: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:44:27: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:44:32: 1000000 INFO @ Sat, 15 Jan 2022 18:44:37: 2000000 INFO @ Sat, 15 Jan 2022 18:44:42: 3000000 INFO @ Sat, 15 Jan 2022 18:44:44: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:44:44: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:44:44: #1 total tags in treatment: 1655585 INFO @ Sat, 15 Jan 2022 18:44:44: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:44:44: #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 18:44:44: #1 tags after filtering in treatment: 1191931 INFO @ Sat, 15 Jan 2022 18:44:44: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 18:44:44: #1 finished! INFO @ Sat, 15 Jan 2022 18:44:44: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:44:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:44:44: #2 number of paired peaks: 358 WARNING @ Sat, 15 Jan 2022 18:44:44: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Sat, 15 Jan 2022 18:44:44: start model_add_line... INFO @ Sat, 15 Jan 2022 18:44:44: start X-correlation... INFO @ Sat, 15 Jan 2022 18:44:44: end of X-cor INFO @ Sat, 15 Jan 2022 18:44:44: #2 finished! INFO @ Sat, 15 Jan 2022 18:44:44: #2 predicted fragment length is 2 bps INFO @ Sat, 15 Jan 2022 18:44:44: #2 alternative fragment length(s) may be 2,99,138,192,211,246,269,293,328,384,420,462,508,532,547,571 bps INFO @ Sat, 15 Jan 2022 18:44:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.05_model.r WARNING @ Sat, 15 Jan 2022 18:44:48: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:44:48: #2 You may need to consider one of the other alternative d(s): 2,99,138,192,211,246,269,293,328,384,420,462,508,532,547,571 WARNING @ Sat, 15 Jan 2022 18:44:48: #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 18:44:48: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:44:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:44:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:44:51: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.05_peaks.xls INFO @ Sat, 15 Jan 2022 18:44:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:44:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.05_summits.bed INFO @ Sat, 15 Jan 2022 18:44:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling 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 18:44:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.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 18:44:57: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:44:57: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:45:03: 1000000 INFO @ Sat, 15 Jan 2022 18:45:10: 2000000 INFO @ Sat, 15 Jan 2022 18:45:16: 3000000 INFO @ Sat, 15 Jan 2022 18:45:19: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:45:19: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:45:19: #1 total tags in treatment: 1655585 INFO @ Sat, 15 Jan 2022 18:45:19: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:45:19: #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 18:45:19: #1 tags after filtering in treatment: 1191931 INFO @ Sat, 15 Jan 2022 18:45:19: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 18:45:19: #1 finished! INFO @ Sat, 15 Jan 2022 18:45:19: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:45:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:45:19: #2 number of paired peaks: 358 WARNING @ Sat, 15 Jan 2022 18:45:19: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Sat, 15 Jan 2022 18:45:19: start model_add_line... INFO @ Sat, 15 Jan 2022 18:45:19: start X-correlation... INFO @ Sat, 15 Jan 2022 18:45:19: end of X-cor INFO @ Sat, 15 Jan 2022 18:45:19: #2 finished! INFO @ Sat, 15 Jan 2022 18:45:19: #2 predicted fragment length is 2 bps INFO @ Sat, 15 Jan 2022 18:45:19: #2 alternative fragment length(s) may be 2,99,138,192,211,246,269,293,328,384,420,462,508,532,547,571 bps INFO @ Sat, 15 Jan 2022 18:45:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.10_model.r WARNING @ Sat, 15 Jan 2022 18:45:19: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:45:19: #2 You may need to consider one of the other alternative d(s): 2,99,138,192,211,246,269,293,328,384,420,462,508,532,547,571 WARNING @ Sat, 15 Jan 2022 18:45:19: #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 18:45:19: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:45:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:45:21: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:45:22: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.10_peaks.xls INFO @ Sat, 15 Jan 2022 18:45:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:45:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.10_summits.bed INFO @ Sat, 15 Jan 2022 18:45:23: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling 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 18:45:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.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 18:45:27: #1 read tag files... INFO @ Sat, 15 Jan 2022 18:45:27: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 18:45:32: 1000000 INFO @ Sat, 15 Jan 2022 18:45:37: 2000000 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 18:45:42: 3000000 INFO @ Sat, 15 Jan 2022 18:45:44: #1 tag size is determined as 50 bps INFO @ Sat, 15 Jan 2022 18:45:44: #1 tag size = 50 INFO @ Sat, 15 Jan 2022 18:45:44: #1 total tags in treatment: 1655585 INFO @ Sat, 15 Jan 2022 18:45:44: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 18:45:44: #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 18:45:44: #1 tags after filtering in treatment: 1191931 INFO @ Sat, 15 Jan 2022 18:45:44: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 15 Jan 2022 18:45:44: #1 finished! INFO @ Sat, 15 Jan 2022 18:45:44: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 18:45:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 18:45:45: #2 number of paired peaks: 358 WARNING @ Sat, 15 Jan 2022 18:45:45: Fewer paired peaks (358) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 358 pairs to build model! INFO @ Sat, 15 Jan 2022 18:45:45: start model_add_line... INFO @ Sat, 15 Jan 2022 18:45:45: start X-correlation... INFO @ Sat, 15 Jan 2022 18:45:45: end of X-cor INFO @ Sat, 15 Jan 2022 18:45:45: #2 finished! INFO @ Sat, 15 Jan 2022 18:45:45: #2 predicted fragment length is 2 bps INFO @ Sat, 15 Jan 2022 18:45:45: #2 alternative fragment length(s) may be 2,99,138,192,211,246,269,293,328,384,420,462,508,532,547,571 bps INFO @ Sat, 15 Jan 2022 18:45:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.20_model.r WARNING @ Sat, 15 Jan 2022 18:45:45: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 18:45:45: #2 You may need to consider one of the other alternative d(s): 2,99,138,192,211,246,269,293,328,384,420,462,508,532,547,571 WARNING @ Sat, 15 Jan 2022 18:45:45: #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 18:45:45: #3 Call peaks... INFO @ Sat, 15 Jan 2022 18:45:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 18:45:46: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 18:45:47: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.20_peaks.xls INFO @ Sat, 15 Jan 2022 18:45:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 18:45:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX8398411/SRX8398411.20_summits.bed INFO @ Sat, 15 Jan 2022 18:45:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling