Job ID = 12265238 SRX = SRX4664617 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 24994992 spots for SRR7813044/SRR7813044.sra Written 24994992 spots for SRR7813044/SRR7813044.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265563 ("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: 00:49:47 24994992 reads; of these: 24994992 (100.00%) were paired; of these: 8001558 (32.01%) aligned concordantly 0 times 9194461 (36.79%) aligned concordantly exactly 1 time 7798973 (31.20%) aligned concordantly >1 times ---- 8001558 pairs aligned concordantly 0 times; of these: 2643732 (33.04%) aligned discordantly 1 time ---- 5357826 pairs aligned 0 times concordantly or discordantly; of these: 10715652 mates make up the pairs; of these: 7190994 (67.11%) aligned 0 times 968094 (9.03%) aligned exactly 1 time 2556564 (23.86%) aligned >1 times 85.62% overall alignment rate Time searching: 00:49:47 Overall time: 00:49:47 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] 4456165 / 19298417 = 0.2309 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 07:21:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.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 07:21:06: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:21:06: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:21:13: 1000000 INFO @ Sat, 03 Apr 2021 07:21:21: 2000000 INFO @ Sat, 03 Apr 2021 07:21:28: 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 07:21:36: 4000000 INFO @ Sat, 03 Apr 2021 07:21:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.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 07:21:36: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:21:36: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:21:43: 5000000 INFO @ Sat, 03 Apr 2021 07:21:45: 1000000 INFO @ Sat, 03 Apr 2021 07:21:51: 6000000 INFO @ Sat, 03 Apr 2021 07:21:54: 2000000 INFO @ Sat, 03 Apr 2021 07:21:59: 7000000 INFO @ Sat, 03 Apr 2021 07:22:03: 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 07:22:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.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 07:22:06: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:22:06: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:22:06: 8000000 INFO @ Sat, 03 Apr 2021 07:22:12: 4000000 INFO @ Sat, 03 Apr 2021 07:22:14: 1000000 INFO @ Sat, 03 Apr 2021 07:22:14: 9000000 INFO @ Sat, 03 Apr 2021 07:22:21: 5000000 INFO @ Sat, 03 Apr 2021 07:22:22: 2000000 INFO @ Sat, 03 Apr 2021 07:22:22: 10000000 INFO @ Sat, 03 Apr 2021 07:22:30: 11000000 INFO @ Sat, 03 Apr 2021 07:22:30: 3000000 INFO @ Sat, 03 Apr 2021 07:22:31: 6000000 INFO @ Sat, 03 Apr 2021 07:22:38: 12000000 INFO @ Sat, 03 Apr 2021 07:22:38: 4000000 INFO @ Sat, 03 Apr 2021 07:22:40: 7000000 INFO @ Sat, 03 Apr 2021 07:22:46: 5000000 INFO @ Sat, 03 Apr 2021 07:22:46: 13000000 INFO @ Sat, 03 Apr 2021 07:22:49: 8000000 INFO @ Sat, 03 Apr 2021 07:22:54: 6000000 INFO @ Sat, 03 Apr 2021 07:22:54: 14000000 INFO @ Sat, 03 Apr 2021 07:22:59: 9000000 INFO @ Sat, 03 Apr 2021 07:23:01: 7000000 INFO @ Sat, 03 Apr 2021 07:23:02: 15000000 INFO @ Sat, 03 Apr 2021 07:23:08: 10000000 INFO @ Sat, 03 Apr 2021 07:23:09: 8000000 INFO @ Sat, 03 Apr 2021 07:23:10: 16000000 INFO @ Sat, 03 Apr 2021 07:23:17: 11000000 INFO @ Sat, 03 Apr 2021 07:23:17: 9000000 INFO @ Sat, 03 Apr 2021 07:23:18: 17000000 INFO @ Sat, 03 Apr 2021 07:23:25: 10000000 INFO @ Sat, 03 Apr 2021 07:23:26: 12000000 INFO @ Sat, 03 Apr 2021 07:23:26: 18000000 INFO @ Sat, 03 Apr 2021 07:23:33: 11000000 INFO @ Sat, 03 Apr 2021 07:23:35: 19000000 INFO @ Sat, 03 Apr 2021 07:23:35: 13000000 INFO @ Sat, 03 Apr 2021 07:23:41: 12000000 INFO @ Sat, 03 Apr 2021 07:23:43: 20000000 INFO @ Sat, 03 Apr 2021 07:23:44: 14000000 INFO @ Sat, 03 Apr 2021 07:23:48: 13000000 INFO @ Sat, 03 Apr 2021 07:23:51: 21000000 INFO @ Sat, 03 Apr 2021 07:23:53: 15000000 INFO @ Sat, 03 Apr 2021 07:23:56: 14000000 INFO @ Sat, 03 Apr 2021 07:23:59: 22000000 INFO @ Sat, 03 Apr 2021 07:24:02: 16000000 INFO @ Sat, 03 Apr 2021 07:24:04: 15000000 INFO @ Sat, 03 Apr 2021 07:24:07: 23000000 INFO @ Sat, 03 Apr 2021 07:24:11: 17000000 INFO @ Sat, 03 Apr 2021 07:24:12: 16000000 INFO @ Sat, 03 Apr 2021 07:24:14: 24000000 INFO @ Sat, 03 Apr 2021 07:24:20: 17000000 INFO @ Sat, 03 Apr 2021 07:24:20: 18000000 INFO @ Sat, 03 Apr 2021 07:24:22: 25000000 INFO @ Sat, 03 Apr 2021 07:24:28: 18000000 INFO @ Sat, 03 Apr 2021 07:24:29: 19000000 INFO @ Sat, 03 Apr 2021 07:24:30: 26000000 INFO @ Sat, 03 Apr 2021 07:24:36: 19000000 INFO @ Sat, 03 Apr 2021 07:24:38: 20000000 INFO @ Sat, 03 Apr 2021 07:24:38: 27000000 INFO @ Sat, 03 Apr 2021 07:24:44: 20000000 INFO @ Sat, 03 Apr 2021 07:24:47: 28000000 INFO @ Sat, 03 Apr 2021 07:24:47: 21000000 INFO @ Sat, 03 Apr 2021 07:24:51: 21000000 INFO @ Sat, 03 Apr 2021 07:24:54: 29000000 INFO @ Sat, 03 Apr 2021 07:24:55: 22000000 INFO @ Sat, 03 Apr 2021 07:24:59: 22000000 INFO @ Sat, 03 Apr 2021 07:25:02: 30000000 INFO @ Sat, 03 Apr 2021 07:25:02: 23000000 INFO @ Sat, 03 Apr 2021 07:25:06: 23000000 INFO @ Sat, 03 Apr 2021 07:25:09: 24000000 INFO @ Sat, 03 Apr 2021 07:25:10: 31000000 INFO @ Sat, 03 Apr 2021 07:25:14: 24000000 INFO @ Sat, 03 Apr 2021 07:25:17: 25000000 INFO @ Sat, 03 Apr 2021 07:25:18: 32000000 INFO @ Sat, 03 Apr 2021 07:25:22: 25000000 INFO @ Sat, 03 Apr 2021 07:25:24: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:25:26: 33000000 INFO @ Sat, 03 Apr 2021 07:25:31: 26000000 INFO @ Sat, 03 Apr 2021 07:25:32: 27000000 INFO @ Sat, 03 Apr 2021 07:25:33: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:25:33: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:25:33: #1 total tags in treatment: 12850099 INFO @ Sat, 03 Apr 2021 07:25:33: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:25:33: #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 07:25:34: #1 tags after filtering in treatment: 10364405 INFO @ Sat, 03 Apr 2021 07:25:34: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 03 Apr 2021 07:25:34: #1 finished! INFO @ Sat, 03 Apr 2021 07:25:34: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:25:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:25:35: #2 number of paired peaks: 229 WARNING @ Sat, 03 Apr 2021 07:25:35: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Sat, 03 Apr 2021 07:25:35: start model_add_line... INFO @ Sat, 03 Apr 2021 07:25:35: start X-correlation... INFO @ Sat, 03 Apr 2021 07:25:35: end of X-cor INFO @ Sat, 03 Apr 2021 07:25:35: #2 finished! INFO @ Sat, 03 Apr 2021 07:25:35: #2 predicted fragment length is 91 bps INFO @ Sat, 03 Apr 2021 07:25:35: #2 alternative fragment length(s) may be 4,91 bps INFO @ Sat, 03 Apr 2021 07:25:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.05_model.r WARNING @ Sat, 03 Apr 2021 07:25:35: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:25:35: #2 You may need to consider one of the other alternative d(s): 4,91 WARNING @ Sat, 03 Apr 2021 07:25:35: #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 07:25:35: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:25:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:25:38: 27000000 INFO @ Sat, 03 Apr 2021 07:25:39: 28000000 INFO @ Sat, 03 Apr 2021 07:25:46: 28000000 INFO @ Sat, 03 Apr 2021 07:25:47: 29000000 INFO @ Sat, 03 Apr 2021 07:25:53: 29000000 INFO @ Sat, 03 Apr 2021 07:25:54: 30000000 INFO @ Sat, 03 Apr 2021 07:26:01: 30000000 INFO @ Sat, 03 Apr 2021 07:26:01: 31000000 INFO @ Sat, 03 Apr 2021 07:26:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:26:08: 31000000 INFO @ Sat, 03 Apr 2021 07:26:09: 32000000 INFO @ Sat, 03 Apr 2021 07:26:16: 32000000 INFO @ Sat, 03 Apr 2021 07:26:16: 33000000 INFO @ Sat, 03 Apr 2021 07:26:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:26:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:26:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.05_summits.bed INFO @ Sat, 03 Apr 2021 07:26:22: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4226 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:26:23: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:26:23: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:26:23: #1 total tags in treatment: 12850099 INFO @ Sat, 03 Apr 2021 07:26:23: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:26:23: #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 07:26:23: #1 tags after filtering in treatment: 10364405 INFO @ Sat, 03 Apr 2021 07:26:23: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 03 Apr 2021 07:26:23: #1 finished! INFO @ Sat, 03 Apr 2021 07:26:23: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:26:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:26:23: 33000000 INFO @ Sat, 03 Apr 2021 07:26:24: #2 number of paired peaks: 229 WARNING @ Sat, 03 Apr 2021 07:26:24: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Sat, 03 Apr 2021 07:26:24: start model_add_line... INFO @ Sat, 03 Apr 2021 07:26:24: start X-correlation... INFO @ Sat, 03 Apr 2021 07:26:24: end of X-cor INFO @ Sat, 03 Apr 2021 07:26:24: #2 finished! INFO @ Sat, 03 Apr 2021 07:26:24: #2 predicted fragment length is 91 bps INFO @ Sat, 03 Apr 2021 07:26:24: #2 alternative fragment length(s) may be 4,91 bps INFO @ Sat, 03 Apr 2021 07:26:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.10_model.r WARNING @ Sat, 03 Apr 2021 07:26:24: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:26:24: #2 You may need to consider one of the other alternative d(s): 4,91 WARNING @ Sat, 03 Apr 2021 07:26:24: #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 07:26:24: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:26:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:26:30: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:26:30: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:26:30: #1 total tags in treatment: 12850099 INFO @ Sat, 03 Apr 2021 07:26:30: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:26:30: #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 07:26:30: #1 tags after filtering in treatment: 10364405 INFO @ Sat, 03 Apr 2021 07:26:30: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 03 Apr 2021 07:26:30: #1 finished! INFO @ Sat, 03 Apr 2021 07:26:30: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:26:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:26:31: #2 number of paired peaks: 229 WARNING @ Sat, 03 Apr 2021 07:26:31: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Sat, 03 Apr 2021 07:26:31: start model_add_line... INFO @ Sat, 03 Apr 2021 07:26:31: start X-correlation... INFO @ Sat, 03 Apr 2021 07:26:31: end of X-cor INFO @ Sat, 03 Apr 2021 07:26:31: #2 finished! INFO @ Sat, 03 Apr 2021 07:26:31: #2 predicted fragment length is 91 bps INFO @ Sat, 03 Apr 2021 07:26:31: #2 alternative fragment length(s) may be 4,91 bps INFO @ Sat, 03 Apr 2021 07:26:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.20_model.r WARNING @ Sat, 03 Apr 2021 07:26:31: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:26:31: #2 You may need to consider one of the other alternative d(s): 4,91 WARNING @ Sat, 03 Apr 2021 07:26:31: #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 07:26:31: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:26:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:26:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:27:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:27:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:27:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:27:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.10_summits.bed INFO @ Sat, 03 Apr 2021 07:27:10: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1926 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:27:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:27:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:27:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4664617/SRX4664617.20_summits.bed INFO @ Sat, 03 Apr 2021 07:27:17: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (608 records, 4 fields): 3 millis CompletedMACS2peakCalling