Job ID = 14171994 SRX = SRX10089734 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18057695 spots for SRR13700621/SRR13700621.sra Written 18057695 spots for SRR13700621/SRR13700621.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172605 ("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: 00:49:53 18057695 reads; of these: 18057695 (100.00%) were paired; of these: 3644339 (20.18%) aligned concordantly 0 times 10753496 (59.55%) aligned concordantly exactly 1 time 3659860 (20.27%) aligned concordantly >1 times ---- 3644339 pairs aligned concordantly 0 times; of these: 132643 (3.64%) aligned discordantly 1 time ---- 3511696 pairs aligned 0 times concordantly or discordantly; of these: 7023392 mates make up the pairs; of these: 5757253 (81.97%) aligned 0 times 601582 (8.57%) aligned exactly 1 time 664557 (9.46%) aligned >1 times 84.06% overall alignment rate Time searching: 00:49:53 Overall time: 00:49:53 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] 1787783 / 10233141 = 0.1747 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 14:49:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.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, 11 Dec 2021 14:49:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:49:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:49:24: 1000000 INFO @ Sat, 11 Dec 2021 14:49:33: 2000000 INFO @ Sat, 11 Dec 2021 14:49:41: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 14:49:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.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, 11 Dec 2021 14:49:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:49:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:49:49: 4000000 INFO @ Sat, 11 Dec 2021 14:49:55: 1000000 INFO @ Sat, 11 Dec 2021 14:49:57: 5000000 INFO @ Sat, 11 Dec 2021 14:50:05: 2000000 INFO @ Sat, 11 Dec 2021 14:50:05: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 14:50:14: 7000000 INFO @ Sat, 11 Dec 2021 14:50:15: 3000000 INFO @ Sat, 11 Dec 2021 14:50:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.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, 11 Dec 2021 14:50:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:50:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:50:22: 8000000 INFO @ Sat, 11 Dec 2021 14:50:25: 4000000 INFO @ Sat, 11 Dec 2021 14:50:27: 1000000 INFO @ Sat, 11 Dec 2021 14:50:31: 9000000 INFO @ Sat, 11 Dec 2021 14:50:36: 5000000 INFO @ Sat, 11 Dec 2021 14:50:38: 2000000 INFO @ Sat, 11 Dec 2021 14:50:40: 10000000 INFO @ Sat, 11 Dec 2021 14:50:46: 6000000 INFO @ Sat, 11 Dec 2021 14:50:48: 11000000 INFO @ Sat, 11 Dec 2021 14:50:50: 3000000 INFO @ Sat, 11 Dec 2021 14:50:57: 7000000 INFO @ Sat, 11 Dec 2021 14:50:57: 12000000 INFO @ Sat, 11 Dec 2021 14:51:01: 4000000 INFO @ Sat, 11 Dec 2021 14:51:05: 13000000 INFO @ Sat, 11 Dec 2021 14:51:08: 8000000 INFO @ Sat, 11 Dec 2021 14:51:12: 5000000 INFO @ Sat, 11 Dec 2021 14:51:14: 14000000 INFO @ Sat, 11 Dec 2021 14:51:18: 9000000 INFO @ Sat, 11 Dec 2021 14:51:23: 15000000 INFO @ Sat, 11 Dec 2021 14:51:24: 6000000 INFO @ Sat, 11 Dec 2021 14:51:29: 10000000 INFO @ Sat, 11 Dec 2021 14:51:31: 16000000 INFO @ Sat, 11 Dec 2021 14:51:36: 7000000 INFO @ Sat, 11 Dec 2021 14:51:39: 11000000 INFO @ Sat, 11 Dec 2021 14:51:40: 17000000 INFO @ Sat, 11 Dec 2021 14:51:48: 8000000 INFO @ Sat, 11 Dec 2021 14:51:48: 18000000 INFO @ Sat, 11 Dec 2021 14:51:50: 12000000 INFO @ Sat, 11 Dec 2021 14:51:57: 19000000 INFO @ Sat, 11 Dec 2021 14:51:59: 9000000 INFO @ Sat, 11 Dec 2021 14:52:01: 13000000 INFO @ Sat, 11 Dec 2021 14:52:05: 20000000 INFO @ Sat, 11 Dec 2021 14:52:11: 14000000 INFO @ Sat, 11 Dec 2021 14:52:12: 10000000 INFO @ Sat, 11 Dec 2021 14:52:14: 21000000 INFO @ Sat, 11 Dec 2021 14:52:21: 15000000 INFO @ Sat, 11 Dec 2021 14:52:23: 22000000 INFO @ Sat, 11 Dec 2021 14:52:24: 11000000 INFO @ Sat, 11 Dec 2021 14:52:31: 16000000 INFO @ Sat, 11 Dec 2021 14:52:32: 23000000 INFO @ Sat, 11 Dec 2021 14:52:36: 12000000 INFO @ Sat, 11 Dec 2021 14:52:40: 24000000 INFO @ Sat, 11 Dec 2021 14:52:42: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:52:48: 13000000 INFO @ Sat, 11 Dec 2021 14:52:49: 25000000 INFO @ Sat, 11 Dec 2021 14:52:52: 18000000 INFO @ Sat, 11 Dec 2021 14:52:57: 26000000 INFO @ Sat, 11 Dec 2021 14:53:00: 14000000 INFO @ Sat, 11 Dec 2021 14:53:02: 19000000 INFO @ Sat, 11 Dec 2021 14:53:04: #1 tag size is determined as 73 bps INFO @ Sat, 11 Dec 2021 14:53:04: #1 tag size = 73 INFO @ Sat, 11 Dec 2021 14:53:04: #1 total tags in treatment: 12627189 INFO @ Sat, 11 Dec 2021 14:53:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:53:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 14:53:04: #1 tags after filtering in treatment: 8379713 INFO @ Sat, 11 Dec 2021 14:53:04: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 11 Dec 2021 14:53:04: #1 finished! INFO @ Sat, 11 Dec 2021 14:53:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:53:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:53:05: #2 number of paired peaks: 2867 INFO @ Sat, 11 Dec 2021 14:53:05: start model_add_line... INFO @ Sat, 11 Dec 2021 14:53:05: start X-correlation... INFO @ Sat, 11 Dec 2021 14:53:05: end of X-cor INFO @ Sat, 11 Dec 2021 14:53:05: #2 finished! INFO @ Sat, 11 Dec 2021 14:53:05: #2 predicted fragment length is 94 bps INFO @ Sat, 11 Dec 2021 14:53:05: #2 alternative fragment length(s) may be 94 bps INFO @ Sat, 11 Dec 2021 14:53:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.05_model.r WARNING @ Sat, 11 Dec 2021 14:53:05: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:53:05: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sat, 11 Dec 2021 14:53:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 14:53:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:53:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:53:12: 15000000 INFO @ Sat, 11 Dec 2021 14:53:12: 20000000 INFO @ Sat, 11 Dec 2021 14:53:22: 21000000 INFO @ Sat, 11 Dec 2021 14:53:24: 16000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:53:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:53:34: 22000000 INFO @ Sat, 11 Dec 2021 14:53:36: 17000000 INFO @ Sat, 11 Dec 2021 14:53:44: 23000000 INFO @ Sat, 11 Dec 2021 14:53:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:53:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:53:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.05_summits.bed INFO @ Sat, 11 Dec 2021 14:53:45: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (16097 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:53:48: 18000000 INFO @ Sat, 11 Dec 2021 14:53:54: 24000000 INFO @ Sat, 11 Dec 2021 14:54:00: 19000000 INFO @ Sat, 11 Dec 2021 14:54:04: 25000000 INFO @ Sat, 11 Dec 2021 14:54:12: 20000000 INFO @ Sat, 11 Dec 2021 14:54:14: 26000000 INFO @ Sat, 11 Dec 2021 14:54:22: #1 tag size is determined as 73 bps INFO @ Sat, 11 Dec 2021 14:54:22: #1 tag size = 73 INFO @ Sat, 11 Dec 2021 14:54:22: #1 total tags in treatment: 12627189 INFO @ Sat, 11 Dec 2021 14:54:22: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:54:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 14:54:23: #1 tags after filtering in treatment: 8379713 INFO @ Sat, 11 Dec 2021 14:54:23: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 11 Dec 2021 14:54:23: #1 finished! INFO @ Sat, 11 Dec 2021 14:54:23: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:54:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:54:24: #2 number of paired peaks: 2867 INFO @ Sat, 11 Dec 2021 14:54:24: start model_add_line... INFO @ Sat, 11 Dec 2021 14:54:24: start X-correlation... INFO @ Sat, 11 Dec 2021 14:54:24: end of X-cor INFO @ Sat, 11 Dec 2021 14:54:24: #2 finished! INFO @ Sat, 11 Dec 2021 14:54:24: #2 predicted fragment length is 94 bps INFO @ Sat, 11 Dec 2021 14:54:24: #2 alternative fragment length(s) may be 94 bps INFO @ Sat, 11 Dec 2021 14:54:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.10_model.r WARNING @ Sat, 11 Dec 2021 14:54:24: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:54:24: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sat, 11 Dec 2021 14:54:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 14:54:24: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:54:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:54:25: 21000000 INFO @ Sat, 11 Dec 2021 14:54:37: 22000000 INFO @ Sat, 11 Dec 2021 14:54:49: 23000000 INFO @ Sat, 11 Dec 2021 14:54:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:55:01: 24000000 INFO @ Sat, 11 Dec 2021 14:55:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:55:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:55:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.10_summits.bed INFO @ Sat, 11 Dec 2021 14:55:02: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10187 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:55:14: 25000000 INFO @ Sat, 11 Dec 2021 14:55:26: 26000000 INFO @ Sat, 11 Dec 2021 14:55:36: #1 tag size is determined as 73 bps INFO @ Sat, 11 Dec 2021 14:55:36: #1 tag size = 73 INFO @ Sat, 11 Dec 2021 14:55:36: #1 total tags in treatment: 12627189 INFO @ Sat, 11 Dec 2021 14:55:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:55:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 14:55:36: #1 tags after filtering in treatment: 8379713 INFO @ Sat, 11 Dec 2021 14:55:36: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 11 Dec 2021 14:55:36: #1 finished! INFO @ Sat, 11 Dec 2021 14:55:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:55:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:55:37: #2 number of paired peaks: 2867 INFO @ Sat, 11 Dec 2021 14:55:37: start model_add_line... INFO @ Sat, 11 Dec 2021 14:55:38: start X-correlation... INFO @ Sat, 11 Dec 2021 14:55:38: end of X-cor INFO @ Sat, 11 Dec 2021 14:55:38: #2 finished! INFO @ Sat, 11 Dec 2021 14:55:38: #2 predicted fragment length is 94 bps INFO @ Sat, 11 Dec 2021 14:55:38: #2 alternative fragment length(s) may be 94 bps INFO @ Sat, 11 Dec 2021 14:55:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.20_model.r WARNING @ Sat, 11 Dec 2021 14:55:38: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:55:38: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sat, 11 Dec 2021 14:55:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 14:55:38: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:55:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:56:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:56:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:56:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:56:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089734/SRX10089734.20_summits.bed INFO @ Sat, 11 Dec 2021 14:56:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4340 records, 4 fields): 7 millis CompletedMACS2peakCalling