Job ID = 16439455 SRX = SRX9518315 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 31632831 spots for SRR13070798/SRR13070798.sra Written 31632831 spots for SRR13070798/SRR13070798.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439878 ("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: 01:06:45 31632831 reads; of these: 31632831 (100.00%) were paired; of these: 15938456 (50.39%) aligned concordantly 0 times 7776704 (24.58%) aligned concordantly exactly 1 time 7917671 (25.03%) aligned concordantly >1 times ---- 15938456 pairs aligned concordantly 0 times; of these: 532643 (3.34%) aligned discordantly 1 time ---- 15405813 pairs aligned 0 times concordantly or discordantly; of these: 30811626 mates make up the pairs; of these: 29103214 (94.46%) aligned 0 times 335954 (1.09%) aligned exactly 1 time 1372458 (4.45%) aligned >1 times 54.00% overall alignment rate Time searching: 01:06:45 Overall time: 01:06:45 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] 6086019 / 16123293 = 0.3775 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:33:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.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, 02 Aug 2022 16:33:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:33:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:33:54: 1000000 INFO @ Tue, 02 Aug 2022 16:34:02: 2000000 INFO @ Tue, 02 Aug 2022 16:34:10: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:34:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.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, 02 Aug 2022 16:34:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:34:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:34:19: 4000000 INFO @ Tue, 02 Aug 2022 16:34:24: 1000000 INFO @ Tue, 02 Aug 2022 16:34:27: 5000000 INFO @ Tue, 02 Aug 2022 16:34:33: 2000000 INFO @ Tue, 02 Aug 2022 16:34:35: 6000000 INFO @ Tue, 02 Aug 2022 16:34:41: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 16:34:44: 7000000 INFO @ Tue, 02 Aug 2022 16:34:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.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, 02 Aug 2022 16:34:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:34:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:34:50: 4000000 INFO @ Tue, 02 Aug 2022 16:34:52: 8000000 INFO @ Tue, 02 Aug 2022 16:34:53: 1000000 INFO @ Tue, 02 Aug 2022 16:34:59: 5000000 INFO @ Tue, 02 Aug 2022 16:35:00: 2000000 INFO @ Tue, 02 Aug 2022 16:35:01: 9000000 INFO @ Tue, 02 Aug 2022 16:35:08: 6000000 INFO @ Tue, 02 Aug 2022 16:35:09: 3000000 INFO @ Tue, 02 Aug 2022 16:35:10: 10000000 INFO @ Tue, 02 Aug 2022 16:35:17: 4000000 INFO @ Tue, 02 Aug 2022 16:35:17: 7000000 INFO @ Tue, 02 Aug 2022 16:35:18: 11000000 INFO @ Tue, 02 Aug 2022 16:35:25: 5000000 INFO @ Tue, 02 Aug 2022 16:35:26: 8000000 INFO @ Tue, 02 Aug 2022 16:35:27: 12000000 INFO @ Tue, 02 Aug 2022 16:35:34: 6000000 INFO @ Tue, 02 Aug 2022 16:35:35: 9000000 INFO @ Tue, 02 Aug 2022 16:35:36: 13000000 INFO @ Tue, 02 Aug 2022 16:35:43: 7000000 INFO @ Tue, 02 Aug 2022 16:35:44: 10000000 INFO @ Tue, 02 Aug 2022 16:35:44: 14000000 INFO @ Tue, 02 Aug 2022 16:35:51: 8000000 INFO @ Tue, 02 Aug 2022 16:35:53: 11000000 INFO @ Tue, 02 Aug 2022 16:35:53: 15000000 INFO @ Tue, 02 Aug 2022 16:36:00: 9000000 INFO @ Tue, 02 Aug 2022 16:36:02: 12000000 INFO @ Tue, 02 Aug 2022 16:36:02: 16000000 INFO @ Tue, 02 Aug 2022 16:36:08: 10000000 INFO @ Tue, 02 Aug 2022 16:36:11: 13000000 INFO @ Tue, 02 Aug 2022 16:36:11: 17000000 INFO @ Tue, 02 Aug 2022 16:36:17: 11000000 INFO @ Tue, 02 Aug 2022 16:36:20: 14000000 INFO @ Tue, 02 Aug 2022 16:36:20: 18000000 INFO @ Tue, 02 Aug 2022 16:36:25: 12000000 INFO @ Tue, 02 Aug 2022 16:36:29: 15000000 INFO @ Tue, 02 Aug 2022 16:36:29: 19000000 INFO @ Tue, 02 Aug 2022 16:36:33: 13000000 INFO @ Tue, 02 Aug 2022 16:36:38: 20000000 INFO @ Tue, 02 Aug 2022 16:36:38: 16000000 INFO @ Tue, 02 Aug 2022 16:36:42: 14000000 INFO @ Tue, 02 Aug 2022 16:36:47: 21000000 INFO @ Tue, 02 Aug 2022 16:36:48: 17000000 INFO @ Tue, 02 Aug 2022 16:36:50: 15000000 INFO @ Tue, 02 Aug 2022 16:36:56: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:36:56: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:36:56: #1 total tags in treatment: 9648342 INFO @ Tue, 02 Aug 2022 16:36:56: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:36:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:36:56: #1 tags after filtering in treatment: 7798234 INFO @ Tue, 02 Aug 2022 16:36:56: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 02 Aug 2022 16:36:56: #1 finished! INFO @ Tue, 02 Aug 2022 16:36:56: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:36:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:36:57: #2 number of paired peaks: 559 WARNING @ Tue, 02 Aug 2022 16:36:57: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Tue, 02 Aug 2022 16:36:57: start model_add_line... INFO @ Tue, 02 Aug 2022 16:36:57: start X-correlation... INFO @ Tue, 02 Aug 2022 16:36:57: 18000000 INFO @ Tue, 02 Aug 2022 16:36:57: end of X-cor INFO @ Tue, 02 Aug 2022 16:36:57: #2 finished! INFO @ Tue, 02 Aug 2022 16:36:57: #2 predicted fragment length is 123 bps INFO @ Tue, 02 Aug 2022 16:36:57: #2 alternative fragment length(s) may be 123 bps INFO @ Tue, 02 Aug 2022 16:36:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.05_model.r WARNING @ Tue, 02 Aug 2022 16:36:57: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:36:57: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Tue, 02 Aug 2022 16:36:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 16:36:57: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:36:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:36:58: 16000000 INFO @ Tue, 02 Aug 2022 16:37:06: 19000000 INFO @ Tue, 02 Aug 2022 16:37:06: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:37:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:37:14: 18000000 INFO @ Tue, 02 Aug 2022 16:37:15: 20000000 INFO @ Tue, 02 Aug 2022 16:37:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:37:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:37:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.05_summits.bed INFO @ Tue, 02 Aug 2022 16:37:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4820 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:37:23: 19000000 INFO @ Tue, 02 Aug 2022 16:37:24: 21000000 INFO @ Tue, 02 Aug 2022 16:37:31: 20000000 INFO @ Tue, 02 Aug 2022 16:37:33: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:37:33: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:37:33: #1 total tags in treatment: 9648342 INFO @ Tue, 02 Aug 2022 16:37:33: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:37:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:37:33: #1 tags after filtering in treatment: 7798234 INFO @ Tue, 02 Aug 2022 16:37:33: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 02 Aug 2022 16:37:33: #1 finished! INFO @ Tue, 02 Aug 2022 16:37:33: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:37:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:37:34: #2 number of paired peaks: 559 WARNING @ Tue, 02 Aug 2022 16:37:34: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Tue, 02 Aug 2022 16:37:34: start model_add_line... INFO @ Tue, 02 Aug 2022 16:37:34: start X-correlation... INFO @ Tue, 02 Aug 2022 16:37:34: end of X-cor INFO @ Tue, 02 Aug 2022 16:37:34: #2 finished! INFO @ Tue, 02 Aug 2022 16:37:34: #2 predicted fragment length is 123 bps INFO @ Tue, 02 Aug 2022 16:37:34: #2 alternative fragment length(s) may be 123 bps INFO @ Tue, 02 Aug 2022 16:37:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.10_model.r WARNING @ Tue, 02 Aug 2022 16:37:34: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:37:34: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Tue, 02 Aug 2022 16:37:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 16:37:34: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:37:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:37:38: 21000000 INFO @ Tue, 02 Aug 2022 16:37:46: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 16:37:46: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 16:37:46: #1 total tags in treatment: 9648342 INFO @ Tue, 02 Aug 2022 16:37:46: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:37:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 16:37:46: #1 tags after filtering in treatment: 7798234 INFO @ Tue, 02 Aug 2022 16:37:46: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 02 Aug 2022 16:37:46: #1 finished! INFO @ Tue, 02 Aug 2022 16:37:46: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:37:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:37:46: #2 number of paired peaks: 559 WARNING @ Tue, 02 Aug 2022 16:37:46: Fewer paired peaks (559) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 559 pairs to build model! INFO @ Tue, 02 Aug 2022 16:37:46: start model_add_line... INFO @ Tue, 02 Aug 2022 16:37:47: start X-correlation... INFO @ Tue, 02 Aug 2022 16:37:47: end of X-cor INFO @ Tue, 02 Aug 2022 16:37:47: #2 finished! INFO @ Tue, 02 Aug 2022 16:37:47: #2 predicted fragment length is 123 bps INFO @ Tue, 02 Aug 2022 16:37:47: #2 alternative fragment length(s) may be 123 bps INFO @ Tue, 02 Aug 2022 16:37:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.20_model.r WARNING @ Tue, 02 Aug 2022 16:37:47: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:37:47: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Tue, 02 Aug 2022 16:37:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 16:37:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:37:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:37:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:38:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:38:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:38:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.10_summits.bed INFO @ Tue, 02 Aug 2022 16:38:00: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2185 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:38:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:38:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:38:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:38:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518315/SRX9518315.20_summits.bed INFO @ Tue, 02 Aug 2022 16:38:10: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (878 records, 4 fields): 141 millis CompletedMACS2peakCalling