Job ID = 12265570 SRX = SRX7277029 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21458846 spots for SRR10597294/SRR10597294.sra Written 21458846 spots for SRR10597294/SRR10597294.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265819 ("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: 00:34:48 21458846 reads; of these: 21458846 (100.00%) were paired; of these: 8166569 (38.06%) aligned concordantly 0 times 9116730 (42.48%) aligned concordantly exactly 1 time 4175547 (19.46%) aligned concordantly >1 times ---- 8166569 pairs aligned concordantly 0 times; of these: 2090172 (25.59%) aligned discordantly 1 time ---- 6076397 pairs aligned 0 times concordantly or discordantly; of these: 12152794 mates make up the pairs; of these: 9747223 (80.21%) aligned 0 times 682316 (5.61%) aligned exactly 1 time 1723255 (14.18%) aligned >1 times 77.29% overall alignment rate Time searching: 00:34:48 Overall time: 00:34:48 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] 2448274 / 15266306 = 0.1604 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 08:29:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.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 08:29:32: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:29:32: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:29:38: 1000000 INFO @ Sat, 03 Apr 2021 08:29:44: 2000000 INFO @ Sat, 03 Apr 2021 08:29:50: 3000000 INFO @ Sat, 03 Apr 2021 08:29:56: 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 08:30:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.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 08:30:02: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:30:02: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:30:03: 5000000 INFO @ Sat, 03 Apr 2021 08:30:09: 1000000 INFO @ Sat, 03 Apr 2021 08:30:10: 6000000 INFO @ Sat, 03 Apr 2021 08:30:17: 2000000 INFO @ Sat, 03 Apr 2021 08:30:17: 7000000 INFO @ Sat, 03 Apr 2021 08:30:24: 8000000 INFO @ Sat, 03 Apr 2021 08:30:24: 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 08:30:31: 9000000 INFO @ Sat, 03 Apr 2021 08:30:31: 4000000 INFO @ Sat, 03 Apr 2021 08:30:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.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 08:30:32: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:30:32: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:30:39: 10000000 INFO @ Sat, 03 Apr 2021 08:30:39: 5000000 INFO @ Sat, 03 Apr 2021 08:30:40: 1000000 INFO @ Sat, 03 Apr 2021 08:30:46: 11000000 INFO @ Sat, 03 Apr 2021 08:30:47: 6000000 INFO @ Sat, 03 Apr 2021 08:30:48: 2000000 INFO @ Sat, 03 Apr 2021 08:30:54: 12000000 INFO @ Sat, 03 Apr 2021 08:30:55: 7000000 INFO @ Sat, 03 Apr 2021 08:30:57: 3000000 INFO @ Sat, 03 Apr 2021 08:31:02: 13000000 INFO @ Sat, 03 Apr 2021 08:31:02: 8000000 INFO @ Sat, 03 Apr 2021 08:31:05: 4000000 INFO @ Sat, 03 Apr 2021 08:31:10: 14000000 INFO @ Sat, 03 Apr 2021 08:31:10: 9000000 INFO @ Sat, 03 Apr 2021 08:31:13: 5000000 INFO @ Sat, 03 Apr 2021 08:31:18: 15000000 INFO @ Sat, 03 Apr 2021 08:31:18: 10000000 INFO @ Sat, 03 Apr 2021 08:31:21: 6000000 INFO @ Sat, 03 Apr 2021 08:31:25: 16000000 INFO @ Sat, 03 Apr 2021 08:31:26: 11000000 INFO @ Sat, 03 Apr 2021 08:31:29: 7000000 INFO @ Sat, 03 Apr 2021 08:31:33: 17000000 INFO @ Sat, 03 Apr 2021 08:31:34: 12000000 INFO @ Sat, 03 Apr 2021 08:31:36: 8000000 INFO @ Sat, 03 Apr 2021 08:31:40: 18000000 INFO @ Sat, 03 Apr 2021 08:31:41: 13000000 INFO @ Sat, 03 Apr 2021 08:31:44: 9000000 INFO @ Sat, 03 Apr 2021 08:31:48: 19000000 INFO @ Sat, 03 Apr 2021 08:31:49: 14000000 INFO @ Sat, 03 Apr 2021 08:31:51: 10000000 INFO @ Sat, 03 Apr 2021 08:31:54: 20000000 INFO @ Sat, 03 Apr 2021 08:31:56: 15000000 INFO @ Sat, 03 Apr 2021 08:31:59: 11000000 INFO @ Sat, 03 Apr 2021 08:32:01: 21000000 INFO @ Sat, 03 Apr 2021 08:32:03: 16000000 INFO @ Sat, 03 Apr 2021 08:32:06: 12000000 INFO @ Sat, 03 Apr 2021 08:32:08: 22000000 INFO @ Sat, 03 Apr 2021 08:32:11: 17000000 INFO @ Sat, 03 Apr 2021 08:32:13: 13000000 INFO @ Sat, 03 Apr 2021 08:32:15: 23000000 INFO @ Sat, 03 Apr 2021 08:32:18: 18000000 INFO @ Sat, 03 Apr 2021 08:32:20: 14000000 INFO @ Sat, 03 Apr 2021 08:32:22: 24000000 INFO @ Sat, 03 Apr 2021 08:32:25: 19000000 INFO @ Sat, 03 Apr 2021 08:32:28: 15000000 INFO @ Sat, 03 Apr 2021 08:32:29: 25000000 INFO @ Sat, 03 Apr 2021 08:32:32: 20000000 INFO @ Sat, 03 Apr 2021 08:32:35: 16000000 INFO @ Sat, 03 Apr 2021 08:32:36: 26000000 INFO @ Sat, 03 Apr 2021 08:32:39: 21000000 INFO @ Sat, 03 Apr 2021 08:32:42: 17000000 INFO @ Sat, 03 Apr 2021 08:32:44: 27000000 INFO @ Sat, 03 Apr 2021 08:32:46: 22000000 INFO @ Sat, 03 Apr 2021 08:32:50: 18000000 INFO @ Sat, 03 Apr 2021 08:32:50: 28000000 INFO @ Sat, 03 Apr 2021 08:32:52: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:32:52: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:32:52: #1 total tags in treatment: 10941815 INFO @ Sat, 03 Apr 2021 08:32:52: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:32:52: #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 08:32:52: 23000000 INFO @ Sat, 03 Apr 2021 08:32:53: #1 tags after filtering in treatment: 8687139 INFO @ Sat, 03 Apr 2021 08:32:53: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 08:32:53: #1 finished! INFO @ Sat, 03 Apr 2021 08:32:53: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:32:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:32:53: #2 number of paired peaks: 532 WARNING @ Sat, 03 Apr 2021 08:32:53: Fewer paired peaks (532) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 532 pairs to build model! INFO @ Sat, 03 Apr 2021 08:32:53: start model_add_line... INFO @ Sat, 03 Apr 2021 08:32:53: start X-correlation... INFO @ Sat, 03 Apr 2021 08:32:53: end of X-cor INFO @ Sat, 03 Apr 2021 08:32:53: #2 finished! INFO @ Sat, 03 Apr 2021 08:32:53: #2 predicted fragment length is 84 bps INFO @ Sat, 03 Apr 2021 08:32:53: #2 alternative fragment length(s) may be 4,84 bps INFO @ Sat, 03 Apr 2021 08:32:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.05_model.r WARNING @ Sat, 03 Apr 2021 08:32:53: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:32:54: #2 You may need to consider one of the other alternative d(s): 4,84 WARNING @ Sat, 03 Apr 2021 08:32:54: #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 08:32:54: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:32:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:32:56: 19000000 INFO @ Sat, 03 Apr 2021 08:32:59: 24000000 INFO @ Sat, 03 Apr 2021 08:33:02: 20000000 INFO @ Sat, 03 Apr 2021 08:33:05: 25000000 INFO @ Sat, 03 Apr 2021 08:33:08: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:33:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:33:11: 26000000 INFO @ Sat, 03 Apr 2021 08:33:14: 22000000 INFO @ Sat, 03 Apr 2021 08:33:18: 27000000 INFO @ Sat, 03 Apr 2021 08:33:20: 23000000 INFO @ Sat, 03 Apr 2021 08:33:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:33:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:33:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.05_summits.bed INFO @ Sat, 03 Apr 2021 08:33:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7388 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:33:24: 28000000 INFO @ Sat, 03 Apr 2021 08:33:25: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:33:25: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:33:25: #1 total tags in treatment: 10941815 INFO @ Sat, 03 Apr 2021 08:33:25: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:33:25: #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 08:33:26: #1 tags after filtering in treatment: 8687139 INFO @ Sat, 03 Apr 2021 08:33:26: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 08:33:26: #1 finished! INFO @ Sat, 03 Apr 2021 08:33:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:33:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:33:26: #2 number of paired peaks: 532 WARNING @ Sat, 03 Apr 2021 08:33:26: Fewer paired peaks (532) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 532 pairs to build model! INFO @ Sat, 03 Apr 2021 08:33:26: start model_add_line... INFO @ Sat, 03 Apr 2021 08:33:26: start X-correlation... INFO @ Sat, 03 Apr 2021 08:33:26: 24000000 INFO @ Sat, 03 Apr 2021 08:33:26: end of X-cor INFO @ Sat, 03 Apr 2021 08:33:26: #2 finished! INFO @ Sat, 03 Apr 2021 08:33:26: #2 predicted fragment length is 84 bps INFO @ Sat, 03 Apr 2021 08:33:26: #2 alternative fragment length(s) may be 4,84 bps INFO @ Sat, 03 Apr 2021 08:33:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.10_model.r WARNING @ Sat, 03 Apr 2021 08:33:26: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:33:26: #2 You may need to consider one of the other alternative d(s): 4,84 WARNING @ Sat, 03 Apr 2021 08:33:26: #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 08:33:26: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:33:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:33:33: 25000000 INFO @ Sat, 03 Apr 2021 08:33:39: 26000000 INFO @ Sat, 03 Apr 2021 08:33:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:33:46: 27000000 INFO @ Sat, 03 Apr 2021 08:33:52: 28000000 INFO @ Sat, 03 Apr 2021 08:33:54: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 08:33:54: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 08:33:54: #1 total tags in treatment: 10941815 INFO @ Sat, 03 Apr 2021 08:33:54: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:33:54: #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 08:33:54: #1 tags after filtering in treatment: 8687139 INFO @ Sat, 03 Apr 2021 08:33:54: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 08:33:54: #1 finished! INFO @ Sat, 03 Apr 2021 08:33:54: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:33:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:33:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:33:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:33:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.10_summits.bed INFO @ Sat, 03 Apr 2021 08:33:55: Done! INFO @ Sat, 03 Apr 2021 08:33:55: #2 number of paired peaks: 532 WARNING @ Sat, 03 Apr 2021 08:33:55: Fewer paired peaks (532) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 532 pairs to build model! INFO @ Sat, 03 Apr 2021 08:33:55: start model_add_line... pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1928 records, 4 fields): 18 millis INFO @ Sat, 03 Apr 2021 08:33:55: start X-correlation... CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:33:55: end of X-cor INFO @ Sat, 03 Apr 2021 08:33:55: #2 finished! INFO @ Sat, 03 Apr 2021 08:33:55: #2 predicted fragment length is 84 bps INFO @ Sat, 03 Apr 2021 08:33:55: #2 alternative fragment length(s) may be 4,84 bps INFO @ Sat, 03 Apr 2021 08:33:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.20_model.r WARNING @ Sat, 03 Apr 2021 08:33:55: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 08:33:55: #2 You may need to consider one of the other alternative d(s): 4,84 WARNING @ Sat, 03 Apr 2021 08:33:55: #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 08:33:55: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:33:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:34:15: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:34:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:34:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:34:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277029/SRX7277029.20_summits.bed INFO @ Sat, 03 Apr 2021 08:34:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (130 records, 4 fields): 2 millis CompletedMACS2peakCalling