Job ID = 16439509 SRX = SRX9518331 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 8805289 spots for SRR13070814/SRR13070814.sra Written 8805289 spots for SRR13070814/SRR13070814.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439659 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:19:44 8805289 reads; of these: 8805289 (100.00%) were paired; of these: 958162 (10.88%) aligned concordantly 0 times 5735701 (65.14%) aligned concordantly exactly 1 time 2111426 (23.98%) aligned concordantly >1 times ---- 958162 pairs aligned concordantly 0 times; of these: 360682 (37.64%) aligned discordantly 1 time ---- 597480 pairs aligned 0 times concordantly or discordantly; of these: 1194960 mates make up the pairs; of these: 786932 (65.85%) aligned 0 times 138657 (11.60%) aligned exactly 1 time 269371 (22.54%) aligned >1 times 95.53% overall alignment rate Time searching: 00:19:45 Overall time: 00:19:45 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] 143183 / 8158043 = 0.0176 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:51:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.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 @ Tue, 02 Aug 2022 15:51:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:51:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:51:37: 1000000 INFO @ Tue, 02 Aug 2022 15:51:44: 2000000 INFO @ Tue, 02 Aug 2022 15:51:52: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:51:59: 4000000 INFO @ Tue, 02 Aug 2022 15:52:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.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 @ Tue, 02 Aug 2022 15:52:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:52:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:52:07: 1000000 INFO @ Tue, 02 Aug 2022 15:52:08: 5000000 INFO @ Tue, 02 Aug 2022 15:52:15: 2000000 INFO @ Tue, 02 Aug 2022 15:52:16: 6000000 INFO @ Tue, 02 Aug 2022 15:52:22: 3000000 INFO @ Tue, 02 Aug 2022 15:52:25: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:52:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.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 @ Tue, 02 Aug 2022 15:52:30: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:52:30: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:52:30: 4000000 INFO @ Tue, 02 Aug 2022 15:52:33: 8000000 INFO @ Tue, 02 Aug 2022 15:52:37: 1000000 INFO @ Tue, 02 Aug 2022 15:52:37: 5000000 INFO @ Tue, 02 Aug 2022 15:52:41: 9000000 INFO @ Tue, 02 Aug 2022 15:52:44: 2000000 INFO @ Tue, 02 Aug 2022 15:52:45: 6000000 INFO @ Tue, 02 Aug 2022 15:52:50: 10000000 INFO @ Tue, 02 Aug 2022 15:52:52: 3000000 INFO @ Tue, 02 Aug 2022 15:52:52: 7000000 INFO @ Tue, 02 Aug 2022 15:52:58: 11000000 INFO @ Tue, 02 Aug 2022 15:52:59: 4000000 INFO @ Tue, 02 Aug 2022 15:53:00: 8000000 INFO @ Tue, 02 Aug 2022 15:53:07: 12000000 INFO @ Tue, 02 Aug 2022 15:53:07: 5000000 INFO @ Tue, 02 Aug 2022 15:53:08: 9000000 INFO @ Tue, 02 Aug 2022 15:53:15: 6000000 INFO @ Tue, 02 Aug 2022 15:53:15: 10000000 INFO @ Tue, 02 Aug 2022 15:53:15: 13000000 INFO @ Tue, 02 Aug 2022 15:53:22: 7000000 INFO @ Tue, 02 Aug 2022 15:53:23: 11000000 INFO @ Tue, 02 Aug 2022 15:53:24: 14000000 INFO @ Tue, 02 Aug 2022 15:53:30: 8000000 INFO @ Tue, 02 Aug 2022 15:53:30: 12000000 INFO @ Tue, 02 Aug 2022 15:53:32: 15000000 INFO @ Tue, 02 Aug 2022 15:53:37: 9000000 INFO @ Tue, 02 Aug 2022 15:53:38: 13000000 INFO @ Tue, 02 Aug 2022 15:53:41: 16000000 INFO @ Tue, 02 Aug 2022 15:53:45: 10000000 INFO @ Tue, 02 Aug 2022 15:53:45: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:53:45: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:53:45: #1 total tags in treatment: 7707415 INFO @ Tue, 02 Aug 2022 15:53:45: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:53:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:53:45: #1 tags after filtering in treatment: 7426946 INFO @ Tue, 02 Aug 2022 15:53:45: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 15:53:45: #1 finished! INFO @ Tue, 02 Aug 2022 15:53:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:53:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:53:46: 14000000 INFO @ Tue, 02 Aug 2022 15:53:46: #2 number of paired peaks: 124 WARNING @ Tue, 02 Aug 2022 15:53:46: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Tue, 02 Aug 2022 15:53:46: start model_add_line... INFO @ Tue, 02 Aug 2022 15:53:46: start X-correlation... INFO @ Tue, 02 Aug 2022 15:53:46: end of X-cor INFO @ Tue, 02 Aug 2022 15:53:46: #2 finished! INFO @ Tue, 02 Aug 2022 15:53:46: #2 predicted fragment length is 147 bps INFO @ Tue, 02 Aug 2022 15:53:46: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 02 Aug 2022 15:53:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.05_model.r WARNING @ Tue, 02 Aug 2022 15:53:46: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:53:46: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Tue, 02 Aug 2022 15:53:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:53:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:53:46: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:53:53: 11000000 INFO @ Tue, 02 Aug 2022 15:53:53: 15000000 INFO @ Tue, 02 Aug 2022 15:54:00: 12000000 INFO @ Tue, 02 Aug 2022 15:54:00: 16000000 INFO @ Tue, 02 Aug 2022 15:54:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:54:04: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:54:04: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:54:04: #1 total tags in treatment: 7707415 INFO @ Tue, 02 Aug 2022 15:54:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:54:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:54:04: #1 tags after filtering in treatment: 7426946 INFO @ Tue, 02 Aug 2022 15:54:04: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 15:54:04: #1 finished! INFO @ Tue, 02 Aug 2022 15:54:04: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:54:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:54:05: #2 number of paired peaks: 124 WARNING @ Tue, 02 Aug 2022 15:54:05: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Tue, 02 Aug 2022 15:54:05: start model_add_line... INFO @ Tue, 02 Aug 2022 15:54:05: start X-correlation... INFO @ Tue, 02 Aug 2022 15:54:05: end of X-cor INFO @ Tue, 02 Aug 2022 15:54:05: #2 finished! INFO @ Tue, 02 Aug 2022 15:54:05: #2 predicted fragment length is 147 bps INFO @ Tue, 02 Aug 2022 15:54:05: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 02 Aug 2022 15:54:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.10_model.r WARNING @ Tue, 02 Aug 2022 15:54:05: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:54:05: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Tue, 02 Aug 2022 15:54:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:54:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:54:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:54:07: 13000000 INFO @ Tue, 02 Aug 2022 15:54:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:54:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:54:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.05_summits.bed INFO @ Tue, 02 Aug 2022 15:54:10: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (923 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:54:14: 14000000 INFO @ Tue, 02 Aug 2022 15:54:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:54:21: 15000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:54:27: 16000000 INFO @ Tue, 02 Aug 2022 15:54:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:54:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:54:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.10_summits.bed INFO @ Tue, 02 Aug 2022 15:54:28: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (474 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:54:31: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:54:31: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:54:31: #1 total tags in treatment: 7707415 INFO @ Tue, 02 Aug 2022 15:54:31: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:54:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:54:31: #1 tags after filtering in treatment: 7426946 INFO @ Tue, 02 Aug 2022 15:54:31: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 02 Aug 2022 15:54:31: #1 finished! INFO @ Tue, 02 Aug 2022 15:54:31: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:54:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:54:31: #2 number of paired peaks: 124 WARNING @ Tue, 02 Aug 2022 15:54:31: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Tue, 02 Aug 2022 15:54:31: start model_add_line... INFO @ Tue, 02 Aug 2022 15:54:31: start X-correlation... INFO @ Tue, 02 Aug 2022 15:54:31: end of X-cor INFO @ Tue, 02 Aug 2022 15:54:31: #2 finished! INFO @ Tue, 02 Aug 2022 15:54:31: #2 predicted fragment length is 147 bps INFO @ Tue, 02 Aug 2022 15:54:31: #2 alternative fragment length(s) may be 147 bps INFO @ Tue, 02 Aug 2022 15:54:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.20_model.r WARNING @ Tue, 02 Aug 2022 15:54:32: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:54:32: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Tue, 02 Aug 2022 15:54:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:54:32: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:54:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:54:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:54:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:54:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:54:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518331/SRX9518331.20_summits.bed INFO @ Tue, 02 Aug 2022 15:54:55: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (254 records, 4 fields): 2 millis CompletedMACS2peakCalling