Job ID = 14168997 SRX = SRX9910787 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 37454016 spots for SRR13498858/SRR13498858.sra Written 37454016 spots for SRR13498858/SRR13498858.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170305 ("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: 01:26:52 37454016 reads; of these: 37454016 (100.00%) were paired; of these: 18629322 (49.74%) aligned concordantly 0 times 8657389 (23.11%) aligned concordantly exactly 1 time 10167305 (27.15%) aligned concordantly >1 times ---- 18629322 pairs aligned concordantly 0 times; of these: 1256494 (6.74%) aligned discordantly 1 time ---- 17372828 pairs aligned 0 times concordantly or discordantly; of these: 34745656 mates make up the pairs; of these: 29010827 (83.49%) aligned 0 times 376741 (1.08%) aligned exactly 1 time 5358088 (15.42%) aligned >1 times 61.27% overall alignment rate Time searching: 01:26:52 Overall time: 01:26:52 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 36 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] 10650058 / 19899907 = 0.5352 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 00:23:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.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 00:23:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:23:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:23:48: 1000000 INFO @ Sat, 11 Dec 2021 00:23:55: 2000000 INFO @ Sat, 11 Dec 2021 00:24:01: 3000000 INFO @ Sat, 11 Dec 2021 00:24:07: 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 00:24:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.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 00:24:12: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:24:12: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:24:14: 5000000 INFO @ Sat, 11 Dec 2021 00:24:19: 1000000 INFO @ Sat, 11 Dec 2021 00:24:20: 6000000 INFO @ Sat, 11 Dec 2021 00:24:26: 2000000 INFO @ Sat, 11 Dec 2021 00:24:27: 7000000 INFO @ Sat, 11 Dec 2021 00:24:32: 3000000 INFO @ Sat, 11 Dec 2021 00:24:34: 8000000 INFO @ Sat, 11 Dec 2021 00:24:39: 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 00:24:41: 9000000 INFO @ Sat, 11 Dec 2021 00:24:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.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 00:24:42: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:24:42: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:24:46: 5000000 INFO @ Sat, 11 Dec 2021 00:24:48: 10000000 INFO @ Sat, 11 Dec 2021 00:24:49: 1000000 INFO @ Sat, 11 Dec 2021 00:24:53: 6000000 INFO @ Sat, 11 Dec 2021 00:24:55: 11000000 INFO @ Sat, 11 Dec 2021 00:24:56: 2000000 INFO @ Sat, 11 Dec 2021 00:25:00: 7000000 INFO @ Sat, 11 Dec 2021 00:25:02: 12000000 INFO @ Sat, 11 Dec 2021 00:25:03: 3000000 INFO @ Sat, 11 Dec 2021 00:25:06: 8000000 INFO @ Sat, 11 Dec 2021 00:25:09: 13000000 INFO @ Sat, 11 Dec 2021 00:25:10: 4000000 INFO @ Sat, 11 Dec 2021 00:25:13: 9000000 INFO @ Sat, 11 Dec 2021 00:25:15: 14000000 INFO @ Sat, 11 Dec 2021 00:25:17: 5000000 INFO @ Sat, 11 Dec 2021 00:25:20: 10000000 INFO @ Sat, 11 Dec 2021 00:25:22: 15000000 INFO @ Sat, 11 Dec 2021 00:25:24: 6000000 INFO @ Sat, 11 Dec 2021 00:25:27: 11000000 INFO @ Sat, 11 Dec 2021 00:25:29: 16000000 INFO @ Sat, 11 Dec 2021 00:25:31: 7000000 INFO @ Sat, 11 Dec 2021 00:25:33: 12000000 INFO @ Sat, 11 Dec 2021 00:25:36: 17000000 INFO @ Sat, 11 Dec 2021 00:25:38: 8000000 INFO @ Sat, 11 Dec 2021 00:25:40: 13000000 INFO @ Sat, 11 Dec 2021 00:25:42: 18000000 INFO @ Sat, 11 Dec 2021 00:25:45: 9000000 INFO @ Sat, 11 Dec 2021 00:25:46: 14000000 INFO @ Sat, 11 Dec 2021 00:25:49: 19000000 INFO @ Sat, 11 Dec 2021 00:25:52: 10000000 INFO @ Sat, 11 Dec 2021 00:25:53: 15000000 INFO @ Sat, 11 Dec 2021 00:25:56: 20000000 INFO @ Sat, 11 Dec 2021 00:25:59: 11000000 INFO @ Sat, 11 Dec 2021 00:26:00: 16000000 INFO @ Sat, 11 Dec 2021 00:26:03: 21000000 INFO @ Sat, 11 Dec 2021 00:26:06: 12000000 INFO @ Sat, 11 Dec 2021 00:26:06: 17000000 INFO @ Sat, 11 Dec 2021 00:26:10: 22000000 INFO @ Sat, 11 Dec 2021 00:26:13: 18000000 INFO @ Sat, 11 Dec 2021 00:26:13: 13000000 INFO @ Sat, 11 Dec 2021 00:26:17: 23000000 INFO @ Sat, 11 Dec 2021 00:26:20: 14000000 INFO @ Sat, 11 Dec 2021 00:26:20: 19000000 INFO @ Sat, 11 Dec 2021 00:26:24: 24000000 INFO @ Sat, 11 Dec 2021 00:26:26: 15000000 INFO @ Sat, 11 Dec 2021 00:26:27: 20000000 INFO @ Sat, 11 Dec 2021 00:26:29: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 00:26:29: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 00:26:29: #1 total tags in treatment: 8607554 INFO @ Sat, 11 Dec 2021 00:26:29: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:26:29: #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 00:26:29: #1 tags after filtering in treatment: 6699130 INFO @ Sat, 11 Dec 2021 00:26:29: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 11 Dec 2021 00:26:29: #1 finished! INFO @ Sat, 11 Dec 2021 00:26:29: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:26:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:26:29: #2 number of paired peaks: 495 WARNING @ Sat, 11 Dec 2021 00:26:29: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Sat, 11 Dec 2021 00:26:29: start model_add_line... INFO @ Sat, 11 Dec 2021 00:26:29: start X-correlation... INFO @ Sat, 11 Dec 2021 00:26:29: end of X-cor INFO @ Sat, 11 Dec 2021 00:26:29: #2 finished! INFO @ Sat, 11 Dec 2021 00:26:29: #2 predicted fragment length is 206 bps INFO @ Sat, 11 Dec 2021 00:26:29: #2 alternative fragment length(s) may be 206 bps INFO @ Sat, 11 Dec 2021 00:26:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.05_model.r WARNING @ Sat, 11 Dec 2021 00:26:29: #2 Since the d (206) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:26:29: #2 You may need to consider one of the other alternative d(s): 206 WARNING @ Sat, 11 Dec 2021 00:26:29: #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 00:26:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:26:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:26:33: 16000000 INFO @ Sat, 11 Dec 2021 00:26:33: 21000000 INFO @ Sat, 11 Dec 2021 00:26:40: 17000000 INFO @ Sat, 11 Dec 2021 00:26:40: 22000000 INFO @ Sat, 11 Dec 2021 00:26:44: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:26:46: 18000000 INFO @ Sat, 11 Dec 2021 00:26:47: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 00:26:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.05_peaks.xls INFO @ Sat, 11 Dec 2021 00:26:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:26:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.05_summits.bed INFO @ Sat, 11 Dec 2021 00:26:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2705 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 00:26:52: 19000000 INFO @ Sat, 11 Dec 2021 00:26:54: 24000000 INFO @ Sat, 11 Dec 2021 00:26:58: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 00:26:58: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 00:26:58: #1 total tags in treatment: 8607554 INFO @ Sat, 11 Dec 2021 00:26:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:26:58: #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 00:26:58: #1 tags after filtering in treatment: 6699130 INFO @ Sat, 11 Dec 2021 00:26:58: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 11 Dec 2021 00:26:58: #1 finished! INFO @ Sat, 11 Dec 2021 00:26:58: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:26:58: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:26:59: #2 number of paired peaks: 495 WARNING @ Sat, 11 Dec 2021 00:26:59: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Sat, 11 Dec 2021 00:26:59: start model_add_line... INFO @ Sat, 11 Dec 2021 00:26:59: start X-correlation... INFO @ Sat, 11 Dec 2021 00:26:59: end of X-cor INFO @ Sat, 11 Dec 2021 00:26:59: #2 finished! INFO @ Sat, 11 Dec 2021 00:26:59: #2 predicted fragment length is 206 bps INFO @ Sat, 11 Dec 2021 00:26:59: #2 alternative fragment length(s) may be 206 bps INFO @ Sat, 11 Dec 2021 00:26:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.10_model.r WARNING @ Sat, 11 Dec 2021 00:26:59: #2 Since the d (206) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:26:59: #2 You may need to consider one of the other alternative d(s): 206 WARNING @ Sat, 11 Dec 2021 00:26:59: #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 00:26:59: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:26:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:26:59: 20000000 INFO @ Sat, 11 Dec 2021 00:27:06: 21000000 INFO @ Sat, 11 Dec 2021 00:27:12: 22000000 INFO @ Sat, 11 Dec 2021 00:27:13: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:27:19: 23000000 INFO @ Sat, 11 Dec 2021 00:27:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.10_peaks.xls INFO @ Sat, 11 Dec 2021 00:27:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:27:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.10_summits.bed INFO @ Sat, 11 Dec 2021 00:27:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1220 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 00:27:26: 24000000 INFO @ Sat, 11 Dec 2021 00:27:30: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 00:27:30: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 00:27:30: #1 total tags in treatment: 8607554 INFO @ Sat, 11 Dec 2021 00:27:30: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:27:30: #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 00:27:30: #1 tags after filtering in treatment: 6699130 INFO @ Sat, 11 Dec 2021 00:27:30: #1 Redundant rate of treatment: 0.22 INFO @ Sat, 11 Dec 2021 00:27:30: #1 finished! INFO @ Sat, 11 Dec 2021 00:27:30: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:27:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:27:30: #2 number of paired peaks: 495 WARNING @ Sat, 11 Dec 2021 00:27:30: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Sat, 11 Dec 2021 00:27:30: start model_add_line... INFO @ Sat, 11 Dec 2021 00:27:30: start X-correlation... INFO @ Sat, 11 Dec 2021 00:27:30: end of X-cor INFO @ Sat, 11 Dec 2021 00:27:30: #2 finished! INFO @ Sat, 11 Dec 2021 00:27:30: #2 predicted fragment length is 206 bps INFO @ Sat, 11 Dec 2021 00:27:30: #2 alternative fragment length(s) may be 206 bps INFO @ Sat, 11 Dec 2021 00:27:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.20_model.r WARNING @ Sat, 11 Dec 2021 00:27:30: #2 Since the d (206) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:27:30: #2 You may need to consider one of the other alternative d(s): 206 WARNING @ Sat, 11 Dec 2021 00:27:30: #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 00:27:30: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:27:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:27:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:27:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.20_peaks.xls INFO @ Sat, 11 Dec 2021 00:27:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:27:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910787/SRX9910787.20_summits.bed INFO @ Sat, 11 Dec 2021 00:27:52: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (558 records, 4 fields): 2 millis CompletedMACS2peakCalling