Job ID = 12266645 SRX = SRX7806719 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9501354 spots for SRR11186385/SRR11186385.sra Written 9501354 spots for SRR11186385/SRR11186385.sra fastq に変換しました。 bowtie でマッピング中... Your job 12266939 ("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: 00:19:31 9501354 reads; of these: 9501354 (100.00%) were paired; of these: 4410755 (46.42%) aligned concordantly 0 times 2966196 (31.22%) aligned concordantly exactly 1 time 2124403 (22.36%) aligned concordantly >1 times ---- 4410755 pairs aligned concordantly 0 times; of these: 771744 (17.50%) aligned discordantly 1 time ---- 3639011 pairs aligned 0 times concordantly or discordantly; of these: 7278022 mates make up the pairs; of these: 5822665 (80.00%) aligned 0 times 653750 (8.98%) aligned exactly 1 time 801607 (11.01%) aligned >1 times 69.36% overall alignment rate Time searching: 00:19:31 Overall time: 00:19:31 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] 1082419 / 5829908 = 0.1857 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 09:29:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.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 09:29:19: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:29:19: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:29:28: 1000000 INFO @ Sat, 03 Apr 2021 09:29:37: 2000000 INFO @ Sat, 03 Apr 2021 09:29:46: 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 09:29:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.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 09:29:49: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:29:49: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:29:55: 4000000 INFO @ Sat, 03 Apr 2021 09:29:57: 1000000 INFO @ Sat, 03 Apr 2021 09:30:04: 5000000 INFO @ Sat, 03 Apr 2021 09:30:06: 2000000 INFO @ Sat, 03 Apr 2021 09:30:13: 6000000 INFO @ Sat, 03 Apr 2021 09:30:16: 3000000 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 09:30:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.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 09:30:19: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:30:19: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:30:23: 7000000 INFO @ Sat, 03 Apr 2021 09:30:25: 4000000 INFO @ Sat, 03 Apr 2021 09:30:30: 1000000 INFO @ Sat, 03 Apr 2021 09:30:33: 8000000 INFO @ Sat, 03 Apr 2021 09:30:34: 5000000 INFO @ Sat, 03 Apr 2021 09:30:41: 9000000 INFO @ Sat, 03 Apr 2021 09:30:42: 2000000 INFO @ Sat, 03 Apr 2021 09:30:43: 6000000 INFO @ Sat, 03 Apr 2021 09:30:49: 10000000 INFO @ Sat, 03 Apr 2021 09:30:52: 7000000 INFO @ Sat, 03 Apr 2021 09:30:54: 3000000 INFO @ Sat, 03 Apr 2021 09:30:57: 11000000 INFO @ Sat, 03 Apr 2021 09:30:58: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:30:58: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:30:58: #1 total tags in treatment: 4051170 INFO @ Sat, 03 Apr 2021 09:30:58: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:30:58: #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 09:30:58: #1 tags after filtering in treatment: 3290646 INFO @ Sat, 03 Apr 2021 09:30:58: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 03 Apr 2021 09:30:58: #1 finished! INFO @ Sat, 03 Apr 2021 09:30:58: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:30:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:30:58: #2 number of paired peaks: 951 WARNING @ Sat, 03 Apr 2021 09:30:58: Fewer paired peaks (951) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 951 pairs to build model! INFO @ Sat, 03 Apr 2021 09:30:58: start model_add_line... INFO @ Sat, 03 Apr 2021 09:30:58: start X-correlation... INFO @ Sat, 03 Apr 2021 09:30:58: end of X-cor INFO @ Sat, 03 Apr 2021 09:30:58: #2 finished! INFO @ Sat, 03 Apr 2021 09:30:58: #2 predicted fragment length is 151 bps INFO @ Sat, 03 Apr 2021 09:30:58: #2 alternative fragment length(s) may be 151 bps INFO @ Sat, 03 Apr 2021 09:30:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.05_model.r WARNING @ Sat, 03 Apr 2021 09:30:58: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:30:58: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Sat, 03 Apr 2021 09:30:58: #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 09:30:58: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:30:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:30:59: 8000000 INFO @ Sat, 03 Apr 2021 09:31:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:31:05: 4000000 INFO @ Sat, 03 Apr 2021 09:31:06: 9000000 INFO @ Sat, 03 Apr 2021 09:31:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:31:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:31:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.05_summits.bed INFO @ Sat, 03 Apr 2021 09:31:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2665 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:31:13: 10000000 INFO @ Sat, 03 Apr 2021 09:31:17: 5000000 INFO @ Sat, 03 Apr 2021 09:31:20: 11000000 INFO @ Sat, 03 Apr 2021 09:31:20: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:31:20: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:31:20: #1 total tags in treatment: 4051170 INFO @ Sat, 03 Apr 2021 09:31:20: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:31:20: #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 09:31:20: #1 tags after filtering in treatment: 3290646 INFO @ Sat, 03 Apr 2021 09:31:20: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 03 Apr 2021 09:31:20: #1 finished! INFO @ Sat, 03 Apr 2021 09:31:20: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:31:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:31:21: #2 number of paired peaks: 951 WARNING @ Sat, 03 Apr 2021 09:31:21: Fewer paired peaks (951) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 951 pairs to build model! INFO @ Sat, 03 Apr 2021 09:31:21: start model_add_line... INFO @ Sat, 03 Apr 2021 09:31:21: start X-correlation... INFO @ Sat, 03 Apr 2021 09:31:21: end of X-cor INFO @ Sat, 03 Apr 2021 09:31:21: #2 finished! INFO @ Sat, 03 Apr 2021 09:31:21: #2 predicted fragment length is 151 bps INFO @ Sat, 03 Apr 2021 09:31:21: #2 alternative fragment length(s) may be 151 bps INFO @ Sat, 03 Apr 2021 09:31:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.10_model.r WARNING @ Sat, 03 Apr 2021 09:31:21: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:31:21: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Sat, 03 Apr 2021 09:31:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:31:21: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:31:21: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:31:28: 6000000 INFO @ Sat, 03 Apr 2021 09:31:28: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:31:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:31:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:31:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.10_summits.bed INFO @ Sat, 03 Apr 2021 09:31:31: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (924 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:31:38: 7000000 INFO @ Sat, 03 Apr 2021 09:31:49: 8000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 09:31:57: 9000000 INFO @ Sat, 03 Apr 2021 09:32:08: 10000000 INFO @ Sat, 03 Apr 2021 09:32:18: 11000000 INFO @ Sat, 03 Apr 2021 09:32:18: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 09:32:18: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 09:32:18: #1 total tags in treatment: 4051170 INFO @ Sat, 03 Apr 2021 09:32:18: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:32:18: #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 09:32:18: #1 tags after filtering in treatment: 3290646 INFO @ Sat, 03 Apr 2021 09:32:18: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 03 Apr 2021 09:32:18: #1 finished! INFO @ Sat, 03 Apr 2021 09:32:18: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:32:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:32:18: #2 number of paired peaks: 951 WARNING @ Sat, 03 Apr 2021 09:32:18: Fewer paired peaks (951) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 951 pairs to build model! INFO @ Sat, 03 Apr 2021 09:32:18: start model_add_line... INFO @ Sat, 03 Apr 2021 09:32:18: start X-correlation... INFO @ Sat, 03 Apr 2021 09:32:18: end of X-cor INFO @ Sat, 03 Apr 2021 09:32:18: #2 finished! INFO @ Sat, 03 Apr 2021 09:32:18: #2 predicted fragment length is 151 bps INFO @ Sat, 03 Apr 2021 09:32:18: #2 alternative fragment length(s) may be 151 bps INFO @ Sat, 03 Apr 2021 09:32:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.20_model.r WARNING @ Sat, 03 Apr 2021 09:32:18: #2 Since the d (151) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:32:18: #2 You may need to consider one of the other alternative d(s): 151 WARNING @ Sat, 03 Apr 2021 09:32:18: #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 09:32:18: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:32:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:32:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:32:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:32:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:32:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7806719/SRX7806719.20_summits.bed INFO @ Sat, 03 Apr 2021 09:32:29: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (268 records, 4 fields): 2 millis CompletedMACS2peakCalling