Job ID = 14171988 SRX = SRX10089730 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23890190 spots for SRR13700617/SRR13700617.sra Written 23890190 spots for SRR13700617/SRR13700617.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172575 ("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: 00:41:54 23890190 reads; of these: 23890190 (100.00%) were paired; of these: 3244453 (13.58%) aligned concordantly 0 times 15732499 (65.85%) aligned concordantly exactly 1 time 4913238 (20.57%) aligned concordantly >1 times ---- 3244453 pairs aligned concordantly 0 times; of these: 207635 (6.40%) aligned discordantly 1 time ---- 3036818 pairs aligned 0 times concordantly or discordantly; of these: 6073636 mates make up the pairs; of these: 4983984 (82.06%) aligned 0 times 572361 (9.42%) aligned exactly 1 time 517291 (8.52%) aligned >1 times 89.57% overall alignment rate Time searching: 00:41:54 Overall time: 00:41:54 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 20 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] 2422270 / 14373486 = 0.1685 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 14:38:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.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 14:38:23: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:38:23: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:38:28: 1000000 INFO @ Sat, 11 Dec 2021 14:38:33: 2000000 INFO @ Sat, 11 Dec 2021 14:38:39: 3000000 INFO @ Sat, 11 Dec 2021 14:38:44: 4000000 INFO @ Sat, 11 Dec 2021 14:38:49: 5000000 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 14:38:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.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 14:38:53: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:38:53: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:38:55: 6000000 INFO @ Sat, 11 Dec 2021 14:38:59: 1000000 INFO @ Sat, 11 Dec 2021 14:39:01: 7000000 INFO @ Sat, 11 Dec 2021 14:39:05: 2000000 INFO @ Sat, 11 Dec 2021 14:39:07: 8000000 INFO @ Sat, 11 Dec 2021 14:39:11: 3000000 INFO @ Sat, 11 Dec 2021 14:39:13: 9000000 INFO @ Sat, 11 Dec 2021 14:39:17: 4000000 INFO @ Sat, 11 Dec 2021 14:39:18: 10000000 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 14:39:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.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 14:39:23: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:39:23: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:39:23: 5000000 INFO @ Sat, 11 Dec 2021 14:39:24: 11000000 INFO @ Sat, 11 Dec 2021 14:39:29: 6000000 INFO @ Sat, 11 Dec 2021 14:39:30: 1000000 INFO @ Sat, 11 Dec 2021 14:39:31: 12000000 INFO @ Sat, 11 Dec 2021 14:39:36: 7000000 INFO @ Sat, 11 Dec 2021 14:39:37: 13000000 INFO @ Sat, 11 Dec 2021 14:39:37: 2000000 INFO @ Sat, 11 Dec 2021 14:39:42: 8000000 INFO @ Sat, 11 Dec 2021 14:39:43: 14000000 INFO @ Sat, 11 Dec 2021 14:39:44: 3000000 INFO @ Sat, 11 Dec 2021 14:39:48: 9000000 INFO @ Sat, 11 Dec 2021 14:39:50: 15000000 INFO @ Sat, 11 Dec 2021 14:39:52: 4000000 INFO @ Sat, 11 Dec 2021 14:39:54: 10000000 INFO @ Sat, 11 Dec 2021 14:39:56: 16000000 INFO @ Sat, 11 Dec 2021 14:39:59: 5000000 INFO @ Sat, 11 Dec 2021 14:40:01: 11000000 INFO @ Sat, 11 Dec 2021 14:40:02: 17000000 INFO @ Sat, 11 Dec 2021 14:40:06: 6000000 INFO @ Sat, 11 Dec 2021 14:40:07: 12000000 INFO @ Sat, 11 Dec 2021 14:40:08: 18000000 INFO @ Sat, 11 Dec 2021 14:40:13: 7000000 INFO @ Sat, 11 Dec 2021 14:40:14: 13000000 INFO @ Sat, 11 Dec 2021 14:40:15: 19000000 INFO @ Sat, 11 Dec 2021 14:40:20: 14000000 INFO @ Sat, 11 Dec 2021 14:40:20: 8000000 INFO @ Sat, 11 Dec 2021 14:40:21: 20000000 INFO @ Sat, 11 Dec 2021 14:40:26: 15000000 INFO @ Sat, 11 Dec 2021 14:40:27: 21000000 INFO @ Sat, 11 Dec 2021 14:40:27: 9000000 INFO @ Sat, 11 Dec 2021 14:40:33: 16000000 INFO @ Sat, 11 Dec 2021 14:40:33: 22000000 INFO @ Sat, 11 Dec 2021 14:40:34: 10000000 INFO @ Sat, 11 Dec 2021 14:40:39: 17000000 INFO @ Sat, 11 Dec 2021 14:40:40: 23000000 INFO @ Sat, 11 Dec 2021 14:40:41: 11000000 INFO @ Sat, 11 Dec 2021 14:40:45: 18000000 INFO @ Sat, 11 Dec 2021 14:40:46: 24000000 INFO @ Sat, 11 Dec 2021 14:40:49: 12000000 INFO @ Sat, 11 Dec 2021 14:40:52: 19000000 INFO @ Sat, 11 Dec 2021 14:40:52: 25000000 INFO @ Sat, 11 Dec 2021 14:40:56: 13000000 INFO @ Sat, 11 Dec 2021 14:40:58: 20000000 INFO @ Sat, 11 Dec 2021 14:40:59: 26000000 INFO @ Sat, 11 Dec 2021 14:41:03: 14000000 INFO @ Sat, 11 Dec 2021 14:41:04: 21000000 INFO @ Sat, 11 Dec 2021 14:41:05: 27000000 INFO @ Sat, 11 Dec 2021 14:41:10: 15000000 INFO @ Sat, 11 Dec 2021 14:41:10: 22000000 INFO @ Sat, 11 Dec 2021 14:41:11: 28000000 INFO @ Sat, 11 Dec 2021 14:41:16: 23000000 INFO @ Sat, 11 Dec 2021 14:41:17: 16000000 INFO @ Sat, 11 Dec 2021 14:41:18: 29000000 INFO @ Sat, 11 Dec 2021 14:41:23: 24000000 INFO @ Sat, 11 Dec 2021 14:41:24: 30000000 INFO @ Sat, 11 Dec 2021 14:41:24: 17000000 INFO @ Sat, 11 Dec 2021 14:41:29: 25000000 INFO @ Sat, 11 Dec 2021 14:41:30: 31000000 INFO @ Sat, 11 Dec 2021 14:41:31: 18000000 INFO @ Sat, 11 Dec 2021 14:41:35: 26000000 INFO @ Sat, 11 Dec 2021 14:41:37: 32000000 INFO @ Sat, 11 Dec 2021 14:41:38: 19000000 INFO @ Sat, 11 Dec 2021 14:41:42: 27000000 INFO @ Sat, 11 Dec 2021 14:41:43: 33000000 INFO @ Sat, 11 Dec 2021 14:41:46: 20000000 INFO @ Sat, 11 Dec 2021 14:41:48: 28000000 INFO @ Sat, 11 Dec 2021 14:41:49: 34000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:41:53: 21000000 INFO @ Sat, 11 Dec 2021 14:41:54: 29000000 INFO @ Sat, 11 Dec 2021 14:41:56: 35000000 INFO @ Sat, 11 Dec 2021 14:42:00: 22000000 INFO @ Sat, 11 Dec 2021 14:42:00: 30000000 INFO @ Sat, 11 Dec 2021 14:42:02: 36000000 INFO @ Sat, 11 Dec 2021 14:42:07: 31000000 INFO @ Sat, 11 Dec 2021 14:42:07: 23000000 INFO @ Sat, 11 Dec 2021 14:42:08: 37000000 INFO @ Sat, 11 Dec 2021 14:42:13: 32000000 INFO @ Sat, 11 Dec 2021 14:42:14: 24000000 INFO @ Sat, 11 Dec 2021 14:42:14: #1 tag size is determined as 68 bps INFO @ Sat, 11 Dec 2021 14:42:14: #1 tag size = 68 INFO @ Sat, 11 Dec 2021 14:42:14: #1 total tags in treatment: 18226267 INFO @ Sat, 11 Dec 2021 14:42:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:42:14: #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 14:42:15: #1 tags after filtering in treatment: 12252247 INFO @ Sat, 11 Dec 2021 14:42:15: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 11 Dec 2021 14:42:15: #1 finished! INFO @ Sat, 11 Dec 2021 14:42:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:42:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:42:15: #2 number of paired peaks: 1235 INFO @ Sat, 11 Dec 2021 14:42:15: start model_add_line... INFO @ Sat, 11 Dec 2021 14:42:16: start X-correlation... INFO @ Sat, 11 Dec 2021 14:42:16: end of X-cor INFO @ Sat, 11 Dec 2021 14:42:16: #2 finished! INFO @ Sat, 11 Dec 2021 14:42:16: #2 predicted fragment length is 90 bps INFO @ Sat, 11 Dec 2021 14:42:16: #2 alternative fragment length(s) may be 90 bps INFO @ Sat, 11 Dec 2021 14:42:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.05_model.r WARNING @ Sat, 11 Dec 2021 14:42:16: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:42:16: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sat, 11 Dec 2021 14:42:16: #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 14:42:16: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:42:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:42:19: 33000000 INFO @ Sat, 11 Dec 2021 14:42:21: 25000000 INFO @ Sat, 11 Dec 2021 14:42:26: 34000000 INFO @ Sat, 11 Dec 2021 14:42:28: 26000000 INFO @ Sat, 11 Dec 2021 14:42:32: 35000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:42:35: 27000000 INFO @ Sat, 11 Dec 2021 14:42:38: 36000000 INFO @ Sat, 11 Dec 2021 14:42:39: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:42:42: 28000000 INFO @ Sat, 11 Dec 2021 14:42:44: 37000000 INFO @ Sat, 11 Dec 2021 14:42:50: 29000000 INFO @ Sat, 11 Dec 2021 14:42:50: #1 tag size is determined as 68 bps INFO @ Sat, 11 Dec 2021 14:42:50: #1 tag size = 68 INFO @ Sat, 11 Dec 2021 14:42:50: #1 total tags in treatment: 18226267 INFO @ Sat, 11 Dec 2021 14:42:50: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:42:50: #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 14:42:50: #1 tags after filtering in treatment: 12252247 INFO @ Sat, 11 Dec 2021 14:42:50: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 11 Dec 2021 14:42:50: #1 finished! INFO @ Sat, 11 Dec 2021 14:42:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:42:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:42:51: #2 number of paired peaks: 1235 INFO @ Sat, 11 Dec 2021 14:42:51: start model_add_line... INFO @ Sat, 11 Dec 2021 14:42:51: start X-correlation... INFO @ Sat, 11 Dec 2021 14:42:51: end of X-cor INFO @ Sat, 11 Dec 2021 14:42:51: #2 finished! INFO @ Sat, 11 Dec 2021 14:42:51: #2 predicted fragment length is 90 bps INFO @ Sat, 11 Dec 2021 14:42:51: #2 alternative fragment length(s) may be 90 bps INFO @ Sat, 11 Dec 2021 14:42:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.10_model.r WARNING @ Sat, 11 Dec 2021 14:42:51: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:42:51: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sat, 11 Dec 2021 14:42:51: #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 14:42:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:42:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:42:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:42:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:42:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.05_summits.bed INFO @ Sat, 11 Dec 2021 14:42:52: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (15273 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:42:56: 30000000 INFO @ Sat, 11 Dec 2021 14:43:03: 31000000 INFO @ Sat, 11 Dec 2021 14:43:10: 32000000 INFO @ Sat, 11 Dec 2021 14:43:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:43:17: 33000000 INFO @ Sat, 11 Dec 2021 14:43:23: 34000000 INFO @ Sat, 11 Dec 2021 14:43:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:43:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:43:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.10_summits.bed INFO @ Sat, 11 Dec 2021 14:43:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9384 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:43:30: 35000000 INFO @ Sat, 11 Dec 2021 14:43:36: 36000000 INFO @ Sat, 11 Dec 2021 14:43:42: 37000000 INFO @ Sat, 11 Dec 2021 14:43:48: #1 tag size is determined as 68 bps INFO @ Sat, 11 Dec 2021 14:43:48: #1 tag size = 68 INFO @ Sat, 11 Dec 2021 14:43:48: #1 total tags in treatment: 18226267 INFO @ Sat, 11 Dec 2021 14:43:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:43:48: #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 14:43:49: #1 tags after filtering in treatment: 12252247 INFO @ Sat, 11 Dec 2021 14:43:49: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 11 Dec 2021 14:43:49: #1 finished! INFO @ Sat, 11 Dec 2021 14:43:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:43:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:43:50: #2 number of paired peaks: 1235 INFO @ Sat, 11 Dec 2021 14:43:50: start model_add_line... INFO @ Sat, 11 Dec 2021 14:43:50: start X-correlation... INFO @ Sat, 11 Dec 2021 14:43:50: end of X-cor INFO @ Sat, 11 Dec 2021 14:43:50: #2 finished! INFO @ Sat, 11 Dec 2021 14:43:50: #2 predicted fragment length is 90 bps INFO @ Sat, 11 Dec 2021 14:43:50: #2 alternative fragment length(s) may be 90 bps INFO @ Sat, 11 Dec 2021 14:43:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.20_model.r WARNING @ Sat, 11 Dec 2021 14:43:50: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:43:50: #2 You may need to consider one of the other alternative d(s): 90 WARNING @ Sat, 11 Dec 2021 14:43:50: #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 14:43:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:43:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:44:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:44:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:44:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:44:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10089730/SRX10089730.20_summits.bed INFO @ Sat, 11 Dec 2021 14:44:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3816 records, 4 fields): 4 millis CompletedMACS2peakCalling