Job ID = 6627066 SRX = SRX8347281 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-07-14T00:43:02 prefetch.2.10.7: 1) Downloading 'SRR11795464'... 2020-07-14T00:43:02 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:50:20 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:50:20 prefetch.2.10.7: 1) 'SRR11795464' was downloaded successfully 2020-07-14T00:50:20 prefetch.2.10.7: 'SRR11795464' has 0 unresolved dependencies Read 14899791 spots for SRR11795464/SRR11795464.sra Written 14899791 spots for SRR11795464/SRR11795464.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627384 ("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: 00:33:22 14899791 reads; of these: 14899791 (100.00%) were paired; of these: 4336274 (29.10%) aligned concordantly 0 times 8833544 (59.29%) aligned concordantly exactly 1 time 1729973 (11.61%) aligned concordantly >1 times ---- 4336274 pairs aligned concordantly 0 times; of these: 787224 (18.15%) aligned discordantly 1 time ---- 3549050 pairs aligned 0 times concordantly or discordantly; of these: 7098100 mates make up the pairs; of these: 6467268 (91.11%) aligned 0 times 266928 (3.76%) aligned exactly 1 time 363904 (5.13%) aligned >1 times 78.30% overall alignment rate Time searching: 00:33:22 Overall time: 00:33:22 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 20 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] 4479200 / 11310439 = 0.3960 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:33:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.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, 14 Jul 2020 10:33:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:33:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:33:44: 1000000 INFO @ Tue, 14 Jul 2020 10:33:51: 2000000 INFO @ Tue, 14 Jul 2020 10:33:58: 3000000 INFO @ Tue, 14 Jul 2020 10:34:04: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:34:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.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, 14 Jul 2020 10:34:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:34:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:34:11: 5000000 INFO @ Tue, 14 Jul 2020 10:34:15: 1000000 INFO @ Tue, 14 Jul 2020 10:34:19: 6000000 INFO @ Tue, 14 Jul 2020 10:34:22: 2000000 INFO @ Tue, 14 Jul 2020 10:34:26: 7000000 INFO @ Tue, 14 Jul 2020 10:34:29: 3000000 INFO @ Tue, 14 Jul 2020 10:34:33: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 10:34:37: 4000000 INFO @ Tue, 14 Jul 2020 10:34:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.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, 14 Jul 2020 10:34:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:34:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:34:40: 9000000 INFO @ Tue, 14 Jul 2020 10:34:44: 5000000 INFO @ Tue, 14 Jul 2020 10:34:45: 1000000 INFO @ Tue, 14 Jul 2020 10:34:48: 10000000 INFO @ Tue, 14 Jul 2020 10:34:52: 6000000 INFO @ Tue, 14 Jul 2020 10:34:52: 2000000 INFO @ Tue, 14 Jul 2020 10:34:55: 11000000 INFO @ Tue, 14 Jul 2020 10:34:59: 7000000 INFO @ Tue, 14 Jul 2020 10:35:00: 3000000 INFO @ Tue, 14 Jul 2020 10:35:02: 12000000 INFO @ Tue, 14 Jul 2020 10:35:06: 8000000 INFO @ Tue, 14 Jul 2020 10:35:07: 4000000 INFO @ Tue, 14 Jul 2020 10:35:10: 13000000 INFO @ Tue, 14 Jul 2020 10:35:13: 9000000 INFO @ Tue, 14 Jul 2020 10:35:15: 5000000 INFO @ Tue, 14 Jul 2020 10:35:17: 14000000 INFO @ Tue, 14 Jul 2020 10:35:20: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 10:35:20: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 10:35:20: #1 total tags in treatment: 6264947 INFO @ Tue, 14 Jul 2020 10:35:20: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:35:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:35:20: #1 tags after filtering in treatment: 6099358 INFO @ Tue, 14 Jul 2020 10:35:20: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 14 Jul 2020 10:35:20: #1 finished! INFO @ Tue, 14 Jul 2020 10:35:20: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:35:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:35:20: #2 number of paired peaks: 259 WARNING @ Tue, 14 Jul 2020 10:35:20: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Tue, 14 Jul 2020 10:35:20: start model_add_line... INFO @ Tue, 14 Jul 2020 10:35:20: start X-correlation... INFO @ Tue, 14 Jul 2020 10:35:20: end of X-cor INFO @ Tue, 14 Jul 2020 10:35:20: #2 finished! INFO @ Tue, 14 Jul 2020 10:35:20: #2 predicted fragment length is 196 bps INFO @ Tue, 14 Jul 2020 10:35:20: #2 alternative fragment length(s) may be 196 bps INFO @ Tue, 14 Jul 2020 10:35:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.05_model.r WARNING @ Tue, 14 Jul 2020 10:35:20: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:35:20: #2 You may need to consider one of the other alternative d(s): 196 WARNING @ Tue, 14 Jul 2020 10:35:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:35:20: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:35:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:35:20: 10000000 INFO @ Tue, 14 Jul 2020 10:35:22: 6000000 INFO @ Tue, 14 Jul 2020 10:35:28: 11000000 INFO @ Tue, 14 Jul 2020 10:35:29: 7000000 INFO @ Tue, 14 Jul 2020 10:35:33: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:35:35: 12000000 INFO @ Tue, 14 Jul 2020 10:35:37: 8000000 INFO @ Tue, 14 Jul 2020 10:35:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:35:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:35:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.05_summits.bed INFO @ Tue, 14 Jul 2020 10:35:39: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4966 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:35:42: 13000000 INFO @ Tue, 14 Jul 2020 10:35:44: 9000000 INFO @ Tue, 14 Jul 2020 10:35:50: 14000000 INFO @ Tue, 14 Jul 2020 10:35:51: 10000000 INFO @ Tue, 14 Jul 2020 10:35:52: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 10:35:52: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 10:35:52: #1 total tags in treatment: 6264947 INFO @ Tue, 14 Jul 2020 10:35:52: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:35:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:35:52: #1 tags after filtering in treatment: 6099358 INFO @ Tue, 14 Jul 2020 10:35:52: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 14 Jul 2020 10:35:52: #1 finished! INFO @ Tue, 14 Jul 2020 10:35:52: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:35:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:35:53: #2 number of paired peaks: 259 WARNING @ Tue, 14 Jul 2020 10:35:53: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Tue, 14 Jul 2020 10:35:53: start model_add_line... INFO @ Tue, 14 Jul 2020 10:35:53: start X-correlation... INFO @ Tue, 14 Jul 2020 10:35:53: end of X-cor INFO @ Tue, 14 Jul 2020 10:35:53: #2 finished! INFO @ Tue, 14 Jul 2020 10:35:53: #2 predicted fragment length is 196 bps INFO @ Tue, 14 Jul 2020 10:35:53: #2 alternative fragment length(s) may be 196 bps INFO @ Tue, 14 Jul 2020 10:35:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.10_model.r WARNING @ Tue, 14 Jul 2020 10:35:53: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:35:53: #2 You may need to consider one of the other alternative d(s): 196 WARNING @ Tue, 14 Jul 2020 10:35:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:35:53: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:35:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:35:58: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:36:05: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:36:05: 12000000 INFO @ Tue, 14 Jul 2020 10:36:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:36:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:36:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.10_summits.bed INFO @ Tue, 14 Jul 2020 10:36:11: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1743 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:36:12: 13000000 INFO @ Tue, 14 Jul 2020 10:36:19: 14000000 INFO @ Tue, 14 Jul 2020 10:36:22: #1 tag size is determined as 150 bps INFO @ Tue, 14 Jul 2020 10:36:22: #1 tag size = 150 INFO @ Tue, 14 Jul 2020 10:36:22: #1 total tags in treatment: 6264947 INFO @ Tue, 14 Jul 2020 10:36:22: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:36:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:36:22: #1 tags after filtering in treatment: 6099358 INFO @ Tue, 14 Jul 2020 10:36:22: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 14 Jul 2020 10:36:22: #1 finished! INFO @ Tue, 14 Jul 2020 10:36:22: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:36:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:36:22: #2 number of paired peaks: 259 WARNING @ Tue, 14 Jul 2020 10:36:22: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Tue, 14 Jul 2020 10:36:22: start model_add_line... INFO @ Tue, 14 Jul 2020 10:36:22: start X-correlation... INFO @ Tue, 14 Jul 2020 10:36:22: end of X-cor INFO @ Tue, 14 Jul 2020 10:36:22: #2 finished! INFO @ Tue, 14 Jul 2020 10:36:22: #2 predicted fragment length is 196 bps INFO @ Tue, 14 Jul 2020 10:36:22: #2 alternative fragment length(s) may be 196 bps INFO @ Tue, 14 Jul 2020 10:36:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.20_model.r WARNING @ Tue, 14 Jul 2020 10:36:22: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:36:22: #2 You may need to consider one of the other alternative d(s): 196 WARNING @ Tue, 14 Jul 2020 10:36:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:36:22: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:36:22: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:36:34: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:36:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:36:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:36:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8347281/SRX8347281.20_summits.bed INFO @ Tue, 14 Jul 2020 10:36:41: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (278 records, 4 fields): 2 millis CompletedMACS2peakCalling