Job ID = 12265544 SRX = SRX7277018 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23287537 spots for SRR10597283/SRR10597283.sra Written 23287537 spots for SRR10597283/SRR10597283.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265791 ("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: 00:31:41 23287537 reads; of these: 23287537 (100.00%) were paired; of these: 8674605 (37.25%) aligned concordantly 0 times 9694316 (41.63%) aligned concordantly exactly 1 time 4918616 (21.12%) aligned concordantly >1 times ---- 8674605 pairs aligned concordantly 0 times; of these: 2225032 (25.65%) aligned discordantly 1 time ---- 6449573 pairs aligned 0 times concordantly or discordantly; of these: 12899146 mates make up the pairs; of these: 10239846 (79.38%) aligned 0 times 651594 (5.05%) aligned exactly 1 time 2007706 (15.56%) aligned >1 times 78.01% overall alignment rate Time searching: 00:31:41 Overall time: 00:31:41 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 16 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] 2841531 / 16713813 = 0.1700 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 08:19:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.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 08:19:22: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:19:22: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:19:29: 1000000 INFO @ Sat, 03 Apr 2021 08:19:35: 2000000 INFO @ Sat, 03 Apr 2021 08:19:41: 3000000 INFO @ Sat, 03 Apr 2021 08:19:47: 4000000 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 08:19:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.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 08:19:53: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:19:53: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:19:53: 5000000 INFO @ Sat, 03 Apr 2021 08:19:59: 1000000 INFO @ Sat, 03 Apr 2021 08:19:59: 6000000 INFO @ Sat, 03 Apr 2021 08:20:05: 2000000 INFO @ Sat, 03 Apr 2021 08:20:06: 7000000 INFO @ Sat, 03 Apr 2021 08:20:11: 3000000 INFO @ Sat, 03 Apr 2021 08:20:12: 8000000 INFO @ Sat, 03 Apr 2021 08:20:17: 4000000 INFO @ Sat, 03 Apr 2021 08:20:18: 9000000 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 08:20:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.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 08:20:23: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:20:23: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:20:24: 5000000 INFO @ Sat, 03 Apr 2021 08:20:25: 10000000 INFO @ Sat, 03 Apr 2021 08:20:28: 1000000 INFO @ Sat, 03 Apr 2021 08:20:30: 6000000 INFO @ Sat, 03 Apr 2021 08:20:31: 11000000 INFO @ Sat, 03 Apr 2021 08:20:34: 2000000 INFO @ Sat, 03 Apr 2021 08:20:36: 7000000 INFO @ Sat, 03 Apr 2021 08:20:37: 12000000 INFO @ Sat, 03 Apr 2021 08:20:40: 3000000 INFO @ Sat, 03 Apr 2021 08:20:43: 8000000 INFO @ Sat, 03 Apr 2021 08:20:44: 13000000 INFO @ Sat, 03 Apr 2021 08:20:45: 4000000 INFO @ Sat, 03 Apr 2021 08:20:49: 9000000 INFO @ Sat, 03 Apr 2021 08:20:50: 14000000 INFO @ Sat, 03 Apr 2021 08:20:51: 5000000 INFO @ Sat, 03 Apr 2021 08:20:56: 10000000 INFO @ Sat, 03 Apr 2021 08:20:56: 15000000 INFO @ Sat, 03 Apr 2021 08:20:57: 6000000 INFO @ Sat, 03 Apr 2021 08:21:02: 11000000 INFO @ Sat, 03 Apr 2021 08:21:02: 7000000 INFO @ Sat, 03 Apr 2021 08:21:03: 16000000 INFO @ Sat, 03 Apr 2021 08:21:08: 8000000 INFO @ Sat, 03 Apr 2021 08:21:09: 17000000 INFO @ Sat, 03 Apr 2021 08:21:09: 12000000 INFO @ Sat, 03 Apr 2021 08:21:14: 9000000 INFO @ Sat, 03 Apr 2021 08:21:15: 18000000 INFO @ Sat, 03 Apr 2021 08:21:15: 13000000 INFO @ Sat, 03 Apr 2021 08:21:19: 10000000 INFO @ Sat, 03 Apr 2021 08:21:21: 14000000 INFO @ Sat, 03 Apr 2021 08:21:21: 19000000 INFO @ Sat, 03 Apr 2021 08:21:25: 11000000 INFO @ Sat, 03 Apr 2021 08:21:28: 15000000 INFO @ Sat, 03 Apr 2021 08:21:28: 20000000 INFO @ Sat, 03 Apr 2021 08:21:31: 12000000 INFO @ Sat, 03 Apr 2021 08:21:34: 16000000 INFO @ Sat, 03 Apr 2021 08:21:34: 21000000 INFO @ Sat, 03 Apr 2021 08:21:36: 13000000 INFO @ Sat, 03 Apr 2021 08:21:40: 17000000 INFO @ Sat, 03 Apr 2021 08:21:40: 22000000 INFO @ Sat, 03 Apr 2021 08:21:42: 14000000 INFO @ Sat, 03 Apr 2021 08:21:46: 18000000 INFO @ Sat, 03 Apr 2021 08:21:46: 23000000 INFO @ Sat, 03 Apr 2021 08:21:47: 15000000 INFO @ Sat, 03 Apr 2021 08:21:52: 19000000 INFO @ Sat, 03 Apr 2021 08:21:52: 24000000 INFO @ Sat, 03 Apr 2021 08:21:53: 16000000 INFO @ Sat, 03 Apr 2021 08:21:58: 20000000 INFO @ Sat, 03 Apr 2021 08:21:58: 17000000 INFO @ Sat, 03 Apr 2021 08:21:59: 25000000 INFO @ Sat, 03 Apr 2021 08:22:04: 18000000 INFO @ Sat, 03 Apr 2021 08:22:04: 21000000 INFO @ Sat, 03 Apr 2021 08:22:05: 26000000 INFO @ Sat, 03 Apr 2021 08:22:09: 19000000 INFO @ Sat, 03 Apr 2021 08:22:10: 22000000 INFO @ Sat, 03 Apr 2021 08:22:11: 27000000 INFO @ Sat, 03 Apr 2021 08:22:15: 20000000 INFO @ Sat, 03 Apr 2021 08:22:16: 23000000 INFO @ Sat, 03 Apr 2021 08:22:17: 28000000 INFO @ Sat, 03 Apr 2021 08:22:20: 21000000 INFO @ Sat, 03 Apr 2021 08:22:22: 24000000 INFO @ Sat, 03 Apr 2021 08:22:23: 29000000 INFO @ Sat, 03 Apr 2021 08:22:25: 22000000 INFO @ Sat, 03 Apr 2021 08:22:29: 25000000 INFO @ Sat, 03 Apr 2021 08:22:29: 30000000 INFO @ Sat, 03 Apr 2021 08:22:30: 23000000 INFO @ Sat, 03 Apr 2021 08:22:34: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:22:34: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:22:34: #1 total tags in treatment: 11874162 INFO @ Sat, 03 Apr 2021 08:22:34: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:22:34: #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 08:22:34: #1 tags after filtering in treatment: 9581042 INFO @ Sat, 03 Apr 2021 08:22:34: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 03 Apr 2021 08:22:34: #1 finished! INFO @ Sat, 03 Apr 2021 08:22:34: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:22:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:22:35: #2 number of paired peaks: 183 WARNING @ Sat, 03 Apr 2021 08:22:35: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Sat, 03 Apr 2021 08:22:35: start model_add_line... INFO @ Sat, 03 Apr 2021 08:22:35: start X-correlation... INFO @ Sat, 03 Apr 2021 08:22:35: end of X-cor INFO @ Sat, 03 Apr 2021 08:22:35: #2 finished! INFO @ Sat, 03 Apr 2021 08:22:35: #2 predicted fragment length is 91 bps INFO @ Sat, 03 Apr 2021 08:22:35: #2 alternative fragment length(s) may be 4,91,580,598 bps INFO @ Sat, 03 Apr 2021 08:22:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.05_model.r WARNING @ Sat, 03 Apr 2021 08:22:35: #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 08:22:35: #2 You may need to consider one of the other alternative d(s): 4,91,580,598 WARNING @ Sat, 03 Apr 2021 08:22:35: #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 08:22:35: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:22:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:22:35: 26000000 INFO @ Sat, 03 Apr 2021 08:22:36: 24000000 INFO @ Sat, 03 Apr 2021 08:22:41: 25000000 INFO @ Sat, 03 Apr 2021 08:22:41: 27000000 INFO @ Sat, 03 Apr 2021 08:22:47: 26000000 INFO @ Sat, 03 Apr 2021 08:22:47: 28000000 INFO @ Sat, 03 Apr 2021 08:22:52: 27000000 INFO @ Sat, 03 Apr 2021 08:22:53: 29000000 INFO @ Sat, 03 Apr 2021 08:22:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:22:57: 28000000 INFO @ Sat, 03 Apr 2021 08:23:00: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:23:02: 29000000 INFO @ Sat, 03 Apr 2021 08:23:04: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:23:04: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:23:04: #1 total tags in treatment: 11874162 INFO @ Sat, 03 Apr 2021 08:23:04: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:23:04: #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 08:23:04: #1 tags after filtering in treatment: 9581042 INFO @ Sat, 03 Apr 2021 08:23:04: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 03 Apr 2021 08:23:04: #1 finished! INFO @ Sat, 03 Apr 2021 08:23:04: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:23:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:23:05: #2 number of paired peaks: 183 WARNING @ Sat, 03 Apr 2021 08:23:05: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Sat, 03 Apr 2021 08:23:05: start model_add_line... INFO @ Sat, 03 Apr 2021 08:23:05: start X-correlation... INFO @ Sat, 03 Apr 2021 08:23:05: end of X-cor INFO @ Sat, 03 Apr 2021 08:23:05: #2 finished! INFO @ Sat, 03 Apr 2021 08:23:05: #2 predicted fragment length is 91 bps INFO @ Sat, 03 Apr 2021 08:23:05: #2 alternative fragment length(s) may be 4,91,580,598 bps INFO @ Sat, 03 Apr 2021 08:23:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.10_model.r WARNING @ Sat, 03 Apr 2021 08:23:05: #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 08:23:05: #2 You may need to consider one of the other alternative d(s): 4,91,580,598 WARNING @ Sat, 03 Apr 2021 08:23:05: #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 08:23:05: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:23:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:23:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:23:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:23:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.05_summits.bed INFO @ Sat, 03 Apr 2021 08:23:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5778 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:23:08: 30000000 INFO @ Sat, 03 Apr 2021 08:23:11: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:23:11: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:23:11: #1 total tags in treatment: 11874162 INFO @ Sat, 03 Apr 2021 08:23:11: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:23:11: #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 08:23:11: #1 tags after filtering in treatment: 9581042 INFO @ Sat, 03 Apr 2021 08:23:11: #1 Redundant rate of treatment: 0.19 INFO @ Sat, 03 Apr 2021 08:23:11: #1 finished! INFO @ Sat, 03 Apr 2021 08:23:11: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:23:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:23:12: #2 number of paired peaks: 183 WARNING @ Sat, 03 Apr 2021 08:23:12: Fewer paired peaks (183) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 183 pairs to build model! INFO @ Sat, 03 Apr 2021 08:23:12: start model_add_line... INFO @ Sat, 03 Apr 2021 08:23:12: start X-correlation... INFO @ Sat, 03 Apr 2021 08:23:12: end of X-cor INFO @ Sat, 03 Apr 2021 08:23:12: #2 finished! INFO @ Sat, 03 Apr 2021 08:23:12: #2 predicted fragment length is 91 bps INFO @ Sat, 03 Apr 2021 08:23:12: #2 alternative fragment length(s) may be 4,91,580,598 bps INFO @ Sat, 03 Apr 2021 08:23:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.20_model.r WARNING @ Sat, 03 Apr 2021 08:23:12: #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 08:23:12: #2 You may need to consider one of the other alternative d(s): 4,91,580,598 WARNING @ Sat, 03 Apr 2021 08:23:12: #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 08:23:12: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:23:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:23:26: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:23:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:23:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:23:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:23:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.10_summits.bed INFO @ Sat, 03 Apr 2021 08:23:37: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1135 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:23:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:23:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:23:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277018/SRX7277018.20_summits.bed INFO @ Sat, 03 Apr 2021 08:23:45: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (135 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。