Job ID = 12265351 SRX = SRX6430367 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 34079292 spots for SRR9669874/SRR9669874.sra Written 34079292 spots for SRR9669874/SRR9669874.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265610 ("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: 00:36:58 34079292 reads; of these: 34079292 (100.00%) were paired; of these: 18280077 (53.64%) aligned concordantly 0 times 10213311 (29.97%) aligned concordantly exactly 1 time 5585904 (16.39%) aligned concordantly >1 times ---- 18280077 pairs aligned concordantly 0 times; of these: 1819478 (9.95%) aligned discordantly 1 time ---- 16460599 pairs aligned 0 times concordantly or discordantly; of these: 32921198 mates make up the pairs; of these: 31199654 (94.77%) aligned 0 times 628219 (1.91%) aligned exactly 1 time 1093325 (3.32%) aligned >1 times 54.22% overall alignment rate Time searching: 00:36:58 Overall time: 00:36:58 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] 3244492 / 17388161 = 0.1866 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 07:33:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.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 07:33:05: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:33:05: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:33:14: 1000000 INFO @ Sat, 03 Apr 2021 07:33:23: 2000000 INFO @ Sat, 03 Apr 2021 07:33:31: 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 07:33:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.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 07:33:36: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:33:36: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:33:41: 4000000 INFO @ Sat, 03 Apr 2021 07:33:43: 1000000 INFO @ Sat, 03 Apr 2021 07:33:49: 5000000 INFO @ Sat, 03 Apr 2021 07:33:51: 2000000 INFO @ Sat, 03 Apr 2021 07:33:56: 6000000 INFO @ Sat, 03 Apr 2021 07:33:59: 3000000 INFO @ Sat, 03 Apr 2021 07:34:03: 7000000 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 07:34:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.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 07:34:06: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:34:06: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:34:06: 4000000 INFO @ Sat, 03 Apr 2021 07:34:10: 8000000 INFO @ Sat, 03 Apr 2021 07:34:13: 5000000 INFO @ Sat, 03 Apr 2021 07:34:15: 1000000 INFO @ Sat, 03 Apr 2021 07:34:19: 9000000 INFO @ Sat, 03 Apr 2021 07:34:20: 6000000 INFO @ Sat, 03 Apr 2021 07:34:24: 2000000 INFO @ Sat, 03 Apr 2021 07:34:26: 10000000 INFO @ Sat, 03 Apr 2021 07:34:26: 7000000 INFO @ Sat, 03 Apr 2021 07:34:31: 3000000 INFO @ Sat, 03 Apr 2021 07:34:33: 11000000 INFO @ Sat, 03 Apr 2021 07:34:33: 8000000 INFO @ Sat, 03 Apr 2021 07:34:38: 4000000 INFO @ Sat, 03 Apr 2021 07:34:40: 9000000 INFO @ Sat, 03 Apr 2021 07:34:40: 12000000 INFO @ Sat, 03 Apr 2021 07:34:45: 5000000 INFO @ Sat, 03 Apr 2021 07:34:47: 10000000 INFO @ Sat, 03 Apr 2021 07:34:47: 13000000 INFO @ Sat, 03 Apr 2021 07:34:52: 6000000 INFO @ Sat, 03 Apr 2021 07:34:53: 11000000 INFO @ Sat, 03 Apr 2021 07:34:54: 14000000 INFO @ Sat, 03 Apr 2021 07:34:58: 7000000 INFO @ Sat, 03 Apr 2021 07:35:00: 12000000 INFO @ Sat, 03 Apr 2021 07:35:01: 15000000 INFO @ Sat, 03 Apr 2021 07:35:05: 8000000 INFO @ Sat, 03 Apr 2021 07:35:07: 13000000 INFO @ Sat, 03 Apr 2021 07:35:07: 16000000 INFO @ Sat, 03 Apr 2021 07:35:11: 9000000 INFO @ Sat, 03 Apr 2021 07:35:14: 14000000 INFO @ Sat, 03 Apr 2021 07:35:14: 17000000 INFO @ Sat, 03 Apr 2021 07:35:18: 10000000 INFO @ Sat, 03 Apr 2021 07:35:20: 15000000 INFO @ Sat, 03 Apr 2021 07:35:21: 18000000 INFO @ Sat, 03 Apr 2021 07:35:24: 11000000 INFO @ Sat, 03 Apr 2021 07:35:27: 16000000 INFO @ Sat, 03 Apr 2021 07:35:28: 19000000 INFO @ Sat, 03 Apr 2021 07:35:31: 12000000 INFO @ Sat, 03 Apr 2021 07:35:33: 17000000 INFO @ Sat, 03 Apr 2021 07:35:34: 20000000 INFO @ Sat, 03 Apr 2021 07:35:37: 13000000 INFO @ Sat, 03 Apr 2021 07:35:40: 18000000 INFO @ Sat, 03 Apr 2021 07:35:40: 21000000 INFO @ Sat, 03 Apr 2021 07:35:43: 14000000 INFO @ Sat, 03 Apr 2021 07:35:46: 19000000 INFO @ Sat, 03 Apr 2021 07:35:46: 22000000 INFO @ Sat, 03 Apr 2021 07:35:50: 15000000 INFO @ Sat, 03 Apr 2021 07:35:52: 23000000 INFO @ Sat, 03 Apr 2021 07:35:53: 20000000 INFO @ Sat, 03 Apr 2021 07:35:56: 16000000 INFO @ Sat, 03 Apr 2021 07:35:59: 24000000 INFO @ Sat, 03 Apr 2021 07:35:59: 21000000 INFO @ Sat, 03 Apr 2021 07:36:03: 17000000 INFO @ Sat, 03 Apr 2021 07:36:05: 22000000 INFO @ Sat, 03 Apr 2021 07:36:05: 25000000 INFO @ Sat, 03 Apr 2021 07:36:09: 18000000 INFO @ Sat, 03 Apr 2021 07:36:11: 23000000 INFO @ Sat, 03 Apr 2021 07:36:12: 26000000 INFO @ Sat, 03 Apr 2021 07:36:15: 19000000 INFO @ Sat, 03 Apr 2021 07:36:18: 24000000 INFO @ Sat, 03 Apr 2021 07:36:19: 27000000 INFO @ Sat, 03 Apr 2021 07:36:22: 20000000 INFO @ Sat, 03 Apr 2021 07:36:24: 25000000 INFO @ Sat, 03 Apr 2021 07:36:25: 28000000 INFO @ Sat, 03 Apr 2021 07:36:29: 21000000 INFO @ Sat, 03 Apr 2021 07:36:31: 26000000 INFO @ Sat, 03 Apr 2021 07:36:32: 29000000 INFO @ Sat, 03 Apr 2021 07:36:35: 22000000 INFO @ Sat, 03 Apr 2021 07:36:38: 27000000 INFO @ Sat, 03 Apr 2021 07:36:38: 30000000 INFO @ Sat, 03 Apr 2021 07:36:41: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:36:41: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:36:41: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:36:41: #1 total tags in treatment: 12656467 INFO @ Sat, 03 Apr 2021 07:36:41: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:36:41: #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 07:36:42: #1 tags after filtering in treatment: 10439531 INFO @ Sat, 03 Apr 2021 07:36:42: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 07:36:42: #1 finished! INFO @ Sat, 03 Apr 2021 07:36:42: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:36:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:36:42: #2 number of paired peaks: 102 WARNING @ Sat, 03 Apr 2021 07:36:42: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Sat, 03 Apr 2021 07:36:42: start model_add_line... INFO @ Sat, 03 Apr 2021 07:36:43: start X-correlation... INFO @ Sat, 03 Apr 2021 07:36:43: end of X-cor INFO @ Sat, 03 Apr 2021 07:36:43: #2 finished! INFO @ Sat, 03 Apr 2021 07:36:43: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Apr 2021 07:36:43: #2 alternative fragment length(s) may be 2,55,542,598 bps INFO @ Sat, 03 Apr 2021 07:36:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.05_model.r WARNING @ Sat, 03 Apr 2021 07:36:43: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:36:43: #2 You may need to consider one of the other alternative d(s): 2,55,542,598 WARNING @ Sat, 03 Apr 2021 07:36:43: #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 07:36:43: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:36:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:36:44: 28000000 INFO @ Sat, 03 Apr 2021 07:36:47: 24000000 INFO @ Sat, 03 Apr 2021 07:36:50: 29000000 INFO @ Sat, 03 Apr 2021 07:36:54: 25000000 INFO @ Sat, 03 Apr 2021 07:36:57: 30000000 INFO @ Sat, 03 Apr 2021 07:37:00: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:37:00: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:37:00: #1 total tags in treatment: 12656467 INFO @ Sat, 03 Apr 2021 07:37:00: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:37:00: #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 07:37:00: #1 tags after filtering in treatment: 10439531 INFO @ Sat, 03 Apr 2021 07:37:00: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 07:37:00: #1 finished! INFO @ Sat, 03 Apr 2021 07:37:00: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:37:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:37:00: 26000000 INFO @ Sat, 03 Apr 2021 07:37:01: #2 number of paired peaks: 102 WARNING @ Sat, 03 Apr 2021 07:37:01: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Sat, 03 Apr 2021 07:37:01: start model_add_line... INFO @ Sat, 03 Apr 2021 07:37:01: start X-correlation... INFO @ Sat, 03 Apr 2021 07:37:01: end of X-cor INFO @ Sat, 03 Apr 2021 07:37:01: #2 finished! INFO @ Sat, 03 Apr 2021 07:37:01: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Apr 2021 07:37:01: #2 alternative fragment length(s) may be 2,55,542,598 bps INFO @ Sat, 03 Apr 2021 07:37:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.10_model.r WARNING @ Sat, 03 Apr 2021 07:37:01: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:37:01: #2 You may need to consider one of the other alternative d(s): 2,55,542,598 WARNING @ Sat, 03 Apr 2021 07:37:01: #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 07:37:01: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:37:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:37:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:37:06: 27000000 INFO @ Sat, 03 Apr 2021 07:37:12: 28000000 INFO @ Sat, 03 Apr 2021 07:37:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:37:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:37:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.05_summits.bed INFO @ Sat, 03 Apr 2021 07:37:12: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2234 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:37:17: 29000000 INFO @ Sat, 03 Apr 2021 07:37:20: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:37:23: 30000000 INFO @ Sat, 03 Apr 2021 07:37:25: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:37:25: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:37:25: #1 total tags in treatment: 12656467 INFO @ Sat, 03 Apr 2021 07:37:25: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:37:25: #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 07:37:26: #1 tags after filtering in treatment: 10439531 INFO @ Sat, 03 Apr 2021 07:37:26: #1 Redundant rate of treatment: 0.18 INFO @ Sat, 03 Apr 2021 07:37:26: #1 finished! INFO @ Sat, 03 Apr 2021 07:37:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:37:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:37:26: #2 number of paired peaks: 102 WARNING @ Sat, 03 Apr 2021 07:37:26: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Sat, 03 Apr 2021 07:37:26: start model_add_line... INFO @ Sat, 03 Apr 2021 07:37:26: start X-correlation... INFO @ Sat, 03 Apr 2021 07:37:26: end of X-cor INFO @ Sat, 03 Apr 2021 07:37:26: #2 finished! INFO @ Sat, 03 Apr 2021 07:37:26: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Apr 2021 07:37:26: #2 alternative fragment length(s) may be 2,55,542,598 bps INFO @ Sat, 03 Apr 2021 07:37:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.20_model.r WARNING @ Sat, 03 Apr 2021 07:37:26: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:37:26: #2 You may need to consider one of the other alternative d(s): 2,55,542,598 WARNING @ Sat, 03 Apr 2021 07:37:26: #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 07:37:26: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:37:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:37:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:37:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:37:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.10_summits.bed INFO @ Sat, 03 Apr 2021 07:37:30: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (399 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:37:45: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:37:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:37:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:37:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6430367/SRX6430367.20_summits.bed INFO @ Sat, 03 Apr 2021 07:37:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (45 records, 4 fields): 1 millis CompletedMACS2peakCalling