Job ID = 12266646 SRX = SRX7806720 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12597854 spots for SRR11186386/SRR11186386.sra Written 12597854 spots for SRR11186386/SRR11186386.sra fastq に変換しました。 bowtie でマッピング中... Your job 12266991 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:24:44 12597854 reads; of these: 12597854 (100.00%) were paired; of these: 6732032 (53.44%) aligned concordantly 0 times 4073816 (32.34%) aligned concordantly exactly 1 time 1792006 (14.22%) aligned concordantly >1 times ---- 6732032 pairs aligned concordantly 0 times; of these: 1029990 (15.30%) aligned discordantly 1 time ---- 5702042 pairs aligned 0 times concordantly or discordantly; of these: 11404084 mates make up the pairs; of these: 10113959 (88.69%) aligned 0 times 590093 (5.17%) aligned exactly 1 time 700032 (6.14%) aligned >1 times 59.86% overall alignment rate Time searching: 00:24:44 Overall time: 00:24:44 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 892326 / 6854654 = 0.1302 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, 03 Apr 2021 09:35:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Apr 2021 09:35:34: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:35:34: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:35:42: 1000000 INFO @ Sat, 03 Apr 2021 09:35:50: 2000000 INFO @ Sat, 03 Apr 2021 09:35:59: 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, 03 Apr 2021 09:36:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Apr 2021 09:36:04: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:36:04: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:36:07: 4000000 INFO @ Sat, 03 Apr 2021 09:36:14: 1000000 INFO @ Sat, 03 Apr 2021 09:36:16: 5000000 INFO @ Sat, 03 Apr 2021 09:36:24: 2000000 INFO @ Sat, 03 Apr 2021 09:36:26: 6000000 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, 03 Apr 2021 09:36:33: 3000000 INFO @ Sat, 03 Apr 2021 09:36:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Apr 2021 09:36:35: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:36:35: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:36:36: 7000000 INFO @ Sat, 03 Apr 2021 09:36:43: 4000000 INFO @ Sat, 03 Apr 2021 09:36:46: 1000000 INFO @ Sat, 03 Apr 2021 09:36:46: 8000000 INFO @ Sat, 03 Apr 2021 09:36:54: 5000000 INFO @ Sat, 03 Apr 2021 09:36:56: 2000000 INFO @ Sat, 03 Apr 2021 09:36:57: 9000000 INFO @ Sat, 03 Apr 2021 09:37:04: 6000000 INFO @ Sat, 03 Apr 2021 09:37:07: 3000000 INFO @ Sat, 03 Apr 2021 09:37:08: 10000000 INFO @ Sat, 03 Apr 2021 09:37:15: 7000000 INFO @ Sat, 03 Apr 2021 09:37:18: 4000000 INFO @ Sat, 03 Apr 2021 09:37:19: 11000000 INFO @ Sat, 03 Apr 2021 09:37:26: 8000000 INFO @ Sat, 03 Apr 2021 09:37:30: 12000000 INFO @ Sat, 03 Apr 2021 09:37:30: 5000000 INFO @ Sat, 03 Apr 2021 09:37:38: 9000000 INFO @ Sat, 03 Apr 2021 09:37:39: 13000000 INFO @ Sat, 03 Apr 2021 09:37:41: 6000000 INFO @ Sat, 03 Apr 2021 09:37:41: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:37:41: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:37:41: #1 total tags in treatment: 5037658 INFO @ Sat, 03 Apr 2021 09:37:41: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:37:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:37:41: #1 tags after filtering in treatment: 4333205 INFO @ Sat, 03 Apr 2021 09:37:41: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 03 Apr 2021 09:37:41: #1 finished! INFO @ Sat, 03 Apr 2021 09:37:41: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:37:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:37:41: #2 number of paired peaks: 993 WARNING @ Sat, 03 Apr 2021 09:37:41: Fewer paired peaks (993) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 993 pairs to build model! INFO @ Sat, 03 Apr 2021 09:37:41: start model_add_line... INFO @ Sat, 03 Apr 2021 09:37:42: start X-correlation... INFO @ Sat, 03 Apr 2021 09:37:42: end of X-cor INFO @ Sat, 03 Apr 2021 09:37:42: #2 finished! INFO @ Sat, 03 Apr 2021 09:37:42: #2 predicted fragment length is 136 bps INFO @ Sat, 03 Apr 2021 09:37:42: #2 alternative fragment length(s) may be 136 bps INFO @ Sat, 03 Apr 2021 09:37:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.05_model.r WARNING @ Sat, 03 Apr 2021 09:37:42: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:37:42: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Sat, 03 Apr 2021 09:37:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:37:42: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:37:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:37:48: 10000000 INFO @ Sat, 03 Apr 2021 09:37:51: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:37:51: 7000000 INFO @ Sat, 03 Apr 2021 09:37:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:37:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:37:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.05_summits.bed INFO @ Sat, 03 Apr 2021 09:37:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4198 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:37:58: 11000000 INFO @ Sat, 03 Apr 2021 09:38:02: 8000000 INFO @ Sat, 03 Apr 2021 09:38:09: 12000000 INFO @ Sat, 03 Apr 2021 09:38:12: 9000000 INFO @ Sat, 03 Apr 2021 09:38:18: 13000000 INFO @ Sat, 03 Apr 2021 09:38:20: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:38:20: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:38:20: #1 total tags in treatment: 5037658 INFO @ Sat, 03 Apr 2021 09:38:20: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:38:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:38:20: #1 tags after filtering in treatment: 4333205 INFO @ Sat, 03 Apr 2021 09:38:20: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 03 Apr 2021 09:38:20: #1 finished! INFO @ Sat, 03 Apr 2021 09:38:20: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:38:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:38:20: 10000000 INFO @ Sat, 03 Apr 2021 09:38:20: #2 number of paired peaks: 993 WARNING @ Sat, 03 Apr 2021 09:38:20: Fewer paired peaks (993) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 993 pairs to build model! INFO @ Sat, 03 Apr 2021 09:38:20: start model_add_line... INFO @ Sat, 03 Apr 2021 09:38:20: start X-correlation... INFO @ Sat, 03 Apr 2021 09:38:20: end of X-cor INFO @ Sat, 03 Apr 2021 09:38:20: #2 finished! INFO @ Sat, 03 Apr 2021 09:38:20: #2 predicted fragment length is 136 bps INFO @ Sat, 03 Apr 2021 09:38:20: #2 alternative fragment length(s) may be 136 bps INFO @ Sat, 03 Apr 2021 09:38:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.10_model.r WARNING @ Sat, 03 Apr 2021 09:38:20: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:38:20: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Sat, 03 Apr 2021 09:38:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:38:20: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:38:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:38:28: 11000000 INFO @ Sat, 03 Apr 2021 09:38:29: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:38:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:38:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:38:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.10_summits.bed INFO @ Sat, 03 Apr 2021 09:38:34: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1501 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:38:35: 12000000 INFO @ Sat, 03 Apr 2021 09:38:43: 13000000 INFO @ Sat, 03 Apr 2021 09:38:45: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:38:45: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:38:45: #1 total tags in treatment: 5037658 INFO @ Sat, 03 Apr 2021 09:38:45: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:38:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:38:45: #1 tags after filtering in treatment: 4333205 INFO @ Sat, 03 Apr 2021 09:38:45: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 03 Apr 2021 09:38:45: #1 finished! INFO @ Sat, 03 Apr 2021 09:38:45: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:38:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:38:45: #2 number of paired peaks: 993 WARNING @ Sat, 03 Apr 2021 09:38:45: Fewer paired peaks (993) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 993 pairs to build model! INFO @ Sat, 03 Apr 2021 09:38:45: start model_add_line... INFO @ Sat, 03 Apr 2021 09:38:46: start X-correlation... INFO @ Sat, 03 Apr 2021 09:38:46: end of X-cor INFO @ Sat, 03 Apr 2021 09:38:46: #2 finished! INFO @ Sat, 03 Apr 2021 09:38:46: #2 predicted fragment length is 136 bps INFO @ Sat, 03 Apr 2021 09:38:46: #2 alternative fragment length(s) may be 136 bps INFO @ Sat, 03 Apr 2021 09:38:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.20_model.r WARNING @ Sat, 03 Apr 2021 09:38:46: #2 Since the d (136) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:38:46: #2 You may need to consider one of the other alternative d(s): 136 WARNING @ Sat, 03 Apr 2021 09:38:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:38:46: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:38:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:38:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:38:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:38:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:38:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806720/SRX7806720.20_summits.bed INFO @ Sat, 03 Apr 2021 09:38:59: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (348 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。