Job ID = 14171827 SRX = SRX10386243 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13446751 spots for SRR14009308/SRR14009308.sra Written 13446751 spots for SRR14009308/SRR14009308.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172431 ("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: 00:34:13 13446751 reads; of these: 13446751 (100.00%) were paired; of these: 1282553 (9.54%) aligned concordantly 0 times 6771362 (50.36%) aligned concordantly exactly 1 time 5392836 (40.11%) aligned concordantly >1 times ---- 1282553 pairs aligned concordantly 0 times; of these: 232562 (18.13%) aligned discordantly 1 time ---- 1049991 pairs aligned 0 times concordantly or discordantly; of these: 2099982 mates make up the pairs; of these: 1533041 (73.00%) aligned 0 times 247145 (11.77%) aligned exactly 1 time 319796 (15.23%) aligned >1 times 94.30% overall alignment rate Time searching: 00:34:13 Overall time: 00:34:13 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 12 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] 1499290 / 12362027 = 0.1213 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, 11 Dec 2021 13:44:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.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, 11 Dec 2021 13:44:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:44:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:44:11: 1000000 INFO @ Sat, 11 Dec 2021 13:44:17: 2000000 INFO @ Sat, 11 Dec 2021 13:44:24: 3000000 INFO @ Sat, 11 Dec 2021 13:44:30: 4000000 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, 11 Dec 2021 13:44:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.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, 11 Dec 2021 13:44:34: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:44:34: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:44:37: 5000000 INFO @ Sat, 11 Dec 2021 13:44:41: 1000000 INFO @ Sat, 11 Dec 2021 13:44:45: 6000000 INFO @ Sat, 11 Dec 2021 13:44:47: 2000000 INFO @ Sat, 11 Dec 2021 13:44:52: 7000000 INFO @ Sat, 11 Dec 2021 13:44:54: 3000000 INFO @ Sat, 11 Dec 2021 13:45:00: 8000000 INFO @ Sat, 11 Dec 2021 13:45:01: 4000000 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, 11 Dec 2021 13:45:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.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, 11 Dec 2021 13:45:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:45:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:45:07: 9000000 INFO @ Sat, 11 Dec 2021 13:45:07: 5000000 INFO @ Sat, 11 Dec 2021 13:45:11: 1000000 INFO @ Sat, 11 Dec 2021 13:45:14: 6000000 INFO @ Sat, 11 Dec 2021 13:45:14: 10000000 INFO @ Sat, 11 Dec 2021 13:45:17: 2000000 INFO @ Sat, 11 Dec 2021 13:45:20: 7000000 INFO @ Sat, 11 Dec 2021 13:45:22: 11000000 INFO @ Sat, 11 Dec 2021 13:45:24: 3000000 INFO @ Sat, 11 Dec 2021 13:45:27: 8000000 INFO @ Sat, 11 Dec 2021 13:45:29: 12000000 INFO @ Sat, 11 Dec 2021 13:45:31: 4000000 INFO @ Sat, 11 Dec 2021 13:45:34: 9000000 INFO @ Sat, 11 Dec 2021 13:45:37: 13000000 INFO @ Sat, 11 Dec 2021 13:45:37: 5000000 INFO @ Sat, 11 Dec 2021 13:45:40: 10000000 INFO @ Sat, 11 Dec 2021 13:45:44: 6000000 INFO @ Sat, 11 Dec 2021 13:45:44: 14000000 INFO @ Sat, 11 Dec 2021 13:45:47: 11000000 INFO @ Sat, 11 Dec 2021 13:45:50: 7000000 INFO @ Sat, 11 Dec 2021 13:45:51: 15000000 INFO @ Sat, 11 Dec 2021 13:45:53: 12000000 INFO @ Sat, 11 Dec 2021 13:45:57: 8000000 INFO @ Sat, 11 Dec 2021 13:45:59: 16000000 INFO @ Sat, 11 Dec 2021 13:46:00: 13000000 INFO @ Sat, 11 Dec 2021 13:46:03: 9000000 INFO @ Sat, 11 Dec 2021 13:46:06: 14000000 INFO @ Sat, 11 Dec 2021 13:46:06: 17000000 INFO @ Sat, 11 Dec 2021 13:46:10: 10000000 INFO @ Sat, 11 Dec 2021 13:46:13: 15000000 INFO @ Sat, 11 Dec 2021 13:46:14: 18000000 INFO @ Sat, 11 Dec 2021 13:46:16: 11000000 INFO @ Sat, 11 Dec 2021 13:46:20: 16000000 INFO @ Sat, 11 Dec 2021 13:46:21: 19000000 INFO @ Sat, 11 Dec 2021 13:46:23: 12000000 INFO @ Sat, 11 Dec 2021 13:46:26: 17000000 INFO @ Sat, 11 Dec 2021 13:46:29: 20000000 INFO @ Sat, 11 Dec 2021 13:46:30: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:46:33: 18000000 INFO @ Sat, 11 Dec 2021 13:46:36: 14000000 INFO @ Sat, 11 Dec 2021 13:46:36: 21000000 INFO @ Sat, 11 Dec 2021 13:46:40: 19000000 INFO @ Sat, 11 Dec 2021 13:46:43: 15000000 INFO @ Sat, 11 Dec 2021 13:46:44: 22000000 INFO @ Sat, 11 Dec 2021 13:46:46: 20000000 INFO @ Sat, 11 Dec 2021 13:46:46: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:46:46: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:46:46: #1 total tags in treatment: 10666014 INFO @ Sat, 11 Dec 2021 13:46:46: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:46:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:46:46: #1 tags after filtering in treatment: 8428888 INFO @ Sat, 11 Dec 2021 13:46:46: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 11 Dec 2021 13:46:46: #1 finished! INFO @ Sat, 11 Dec 2021 13:46:46: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:46:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:46:47: #2 number of paired peaks: 583 WARNING @ Sat, 11 Dec 2021 13:46:47: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Sat, 11 Dec 2021 13:46:47: start model_add_line... INFO @ Sat, 11 Dec 2021 13:46:47: start X-correlation... INFO @ Sat, 11 Dec 2021 13:46:47: end of X-cor INFO @ Sat, 11 Dec 2021 13:46:47: #2 finished! INFO @ Sat, 11 Dec 2021 13:46:47: #2 predicted fragment length is 96 bps INFO @ Sat, 11 Dec 2021 13:46:47: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 11 Dec 2021 13:46:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.05_model.r WARNING @ Sat, 11 Dec 2021 13:46:47: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:46:47: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 11 Dec 2021 13:46:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:46:47: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:46:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:46:49: 16000000 INFO @ Sat, 11 Dec 2021 13:46:52: 21000000 INFO @ Sat, 11 Dec 2021 13:46:55: 17000000 INFO @ Sat, 11 Dec 2021 13:46:58: 22000000 INFO @ Sat, 11 Dec 2021 13:46:59: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:46:59: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:46:59: #1 total tags in treatment: 10666014 INFO @ Sat, 11 Dec 2021 13:46:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:46:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:47:00: #1 tags after filtering in treatment: 8428888 INFO @ Sat, 11 Dec 2021 13:47:00: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 11 Dec 2021 13:47:00: #1 finished! INFO @ Sat, 11 Dec 2021 13:47:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:47:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:47:00: 18000000 INFO @ Sat, 11 Dec 2021 13:47:00: #2 number of paired peaks: 583 WARNING @ Sat, 11 Dec 2021 13:47:00: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Sat, 11 Dec 2021 13:47:00: start model_add_line... INFO @ Sat, 11 Dec 2021 13:47:00: start X-correlation... INFO @ Sat, 11 Dec 2021 13:47:00: end of X-cor INFO @ Sat, 11 Dec 2021 13:47:00: #2 finished! INFO @ Sat, 11 Dec 2021 13:47:00: #2 predicted fragment length is 96 bps INFO @ Sat, 11 Dec 2021 13:47:00: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 11 Dec 2021 13:47:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.10_model.r WARNING @ Sat, 11 Dec 2021 13:47:00: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:47:00: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 11 Dec 2021 13:47:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:47:00: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:47:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:47:04: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:47:05: 19000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:47:10: 20000000 INFO @ Sat, 11 Dec 2021 13:47:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:47:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:47:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.05_summits.bed INFO @ Sat, 11 Dec 2021 13:47:12: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1727 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:47:15: 21000000 INFO @ Sat, 11 Dec 2021 13:47:17: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:47:21: 22000000 INFO @ Sat, 11 Dec 2021 13:47:22: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 13:47:22: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 13:47:22: #1 total tags in treatment: 10666014 INFO @ Sat, 11 Dec 2021 13:47:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:47:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 13:47:23: #1 tags after filtering in treatment: 8428888 INFO @ Sat, 11 Dec 2021 13:47:23: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 11 Dec 2021 13:47:23: #1 finished! INFO @ Sat, 11 Dec 2021 13:47:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:47:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:47:23: #2 number of paired peaks: 583 WARNING @ Sat, 11 Dec 2021 13:47:23: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Sat, 11 Dec 2021 13:47:23: start model_add_line... INFO @ Sat, 11 Dec 2021 13:47:23: start X-correlation... INFO @ Sat, 11 Dec 2021 13:47:23: end of X-cor INFO @ Sat, 11 Dec 2021 13:47:23: #2 finished! INFO @ Sat, 11 Dec 2021 13:47:23: #2 predicted fragment length is 96 bps INFO @ Sat, 11 Dec 2021 13:47:23: #2 alternative fragment length(s) may be 96 bps INFO @ Sat, 11 Dec 2021 13:47:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.20_model.r WARNING @ Sat, 11 Dec 2021 13:47:23: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 13:47:23: #2 You may need to consider one of the other alternative d(s): 96 WARNING @ Sat, 11 Dec 2021 13:47:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 13:47:23: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:47:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:47:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:47:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:47:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.10_summits.bed INFO @ Sat, 11 Dec 2021 13:47:26: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1137 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:47:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:47:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:47:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:47:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10386243/SRX10386243.20_summits.bed INFO @ Sat, 11 Dec 2021 13:47:49: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (793 records, 4 fields): 2 millis CompletedMACS2peakCalling