Job ID = 16440063 SRX = SRX10855777 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 36243708 spots for SRR14509964/SRR14509964.sra Written 36243708 spots for SRR14509964/SRR14509964.sra fastq に変換しました。 bowtie でマッピング中... Your job 16441486 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 02:14:31 36243708 reads; of these: 36243708 (100.00%) were paired; of these: 3080817 (8.50%) aligned concordantly 0 times 23759381 (65.55%) aligned concordantly exactly 1 time 9403510 (25.95%) aligned concordantly >1 times ---- 3080817 pairs aligned concordantly 0 times; of these: 634621 (20.60%) aligned discordantly 1 time ---- 2446196 pairs aligned 0 times concordantly or discordantly; of these: 4892392 mates make up the pairs; of these: 3354070 (68.56%) aligned 0 times 928139 (18.97%) aligned exactly 1 time 610183 (12.47%) aligned >1 times 95.37% overall alignment rate Time searching: 02:14:32 Overall time: 02:14:32 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 32 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] 14230146 / 33587587 = 0.4237 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 19:37:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.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 19:37:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 19:37:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 19:37:35: 1000000 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 19:37:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.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 19:37:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 19:37:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 19:37:51: 2000000 INFO @ Tue, 02 Aug 2022 19:38:08: 1000000 INFO @ Tue, 02 Aug 2022 19:38:09: 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 19:38:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.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 19:38:22: #1 read tag files... INFO @ Tue, 02 Aug 2022 19:38:22: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 19:38:26: 2000000 INFO @ Tue, 02 Aug 2022 19:38:28: 4000000 INFO @ Tue, 02 Aug 2022 19:38:39: 1000000 INFO @ Tue, 02 Aug 2022 19:38:45: 3000000 INFO @ Tue, 02 Aug 2022 19:38:48: 5000000 INFO @ Tue, 02 Aug 2022 19:38:55: 2000000 INFO @ Tue, 02 Aug 2022 19:39:04: 4000000 INFO @ Tue, 02 Aug 2022 19:39:07: 6000000 INFO @ Tue, 02 Aug 2022 19:39:12: 3000000 INFO @ Tue, 02 Aug 2022 19:39:22: 5000000 INFO @ Tue, 02 Aug 2022 19:39:23: 7000000 INFO @ Tue, 02 Aug 2022 19:39:31: 4000000 INFO @ Tue, 02 Aug 2022 19:39:39: 6000000 INFO @ Tue, 02 Aug 2022 19:39:39: 8000000 INFO @ Tue, 02 Aug 2022 19:39:48: 5000000 INFO @ Tue, 02 Aug 2022 19:39:54: 7000000 INFO @ Tue, 02 Aug 2022 19:39:55: 9000000 INFO @ Tue, 02 Aug 2022 19:40:05: 6000000 INFO @ Tue, 02 Aug 2022 19:40:10: 8000000 INFO @ Tue, 02 Aug 2022 19:40:10: 10000000 INFO @ Tue, 02 Aug 2022 19:40:20: 7000000 INFO @ Tue, 02 Aug 2022 19:40:25: 9000000 INFO @ Tue, 02 Aug 2022 19:40:27: 11000000 INFO @ Tue, 02 Aug 2022 19:40:36: 8000000 INFO @ Tue, 02 Aug 2022 19:40:41: 10000000 INFO @ Tue, 02 Aug 2022 19:40:44: 12000000 INFO @ Tue, 02 Aug 2022 19:40:51: 9000000 INFO @ Tue, 02 Aug 2022 19:40:57: 11000000 INFO @ Tue, 02 Aug 2022 19:41:00: 13000000 INFO @ Tue, 02 Aug 2022 19:41:07: 10000000 INFO @ Tue, 02 Aug 2022 19:41:12: 12000000 INFO @ Tue, 02 Aug 2022 19:41:16: 14000000 INFO @ Tue, 02 Aug 2022 19:41:23: 11000000 INFO @ Tue, 02 Aug 2022 19:41:28: 13000000 INFO @ Tue, 02 Aug 2022 19:41:32: 15000000 INFO @ Tue, 02 Aug 2022 19:41:39: 12000000 INFO @ Tue, 02 Aug 2022 19:41:44: 14000000 INFO @ Tue, 02 Aug 2022 19:41:48: 16000000 INFO @ Tue, 02 Aug 2022 19:41:55: 13000000 INFO @ Tue, 02 Aug 2022 19:42:00: 15000000 INFO @ Tue, 02 Aug 2022 19:42:03: 17000000 INFO @ Tue, 02 Aug 2022 19:42:10: 14000000 INFO @ Tue, 02 Aug 2022 19:42:14: 16000000 INFO @ Tue, 02 Aug 2022 19:42:18: 18000000 INFO @ Tue, 02 Aug 2022 19:42:25: 15000000 INFO @ Tue, 02 Aug 2022 19:42:29: 17000000 INFO @ Tue, 02 Aug 2022 19:42:34: 19000000 INFO @ Tue, 02 Aug 2022 19:42:39: 16000000 INFO @ Tue, 02 Aug 2022 19:42:44: 18000000 INFO @ Tue, 02 Aug 2022 19:42:49: 20000000 INFO @ Tue, 02 Aug 2022 19:42:54: 17000000 INFO @ Tue, 02 Aug 2022 19:42:58: 19000000 INFO @ Tue, 02 Aug 2022 19:43:04: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 19:43:08: 18000000 INFO @ Tue, 02 Aug 2022 19:43:13: 20000000 INFO @ Tue, 02 Aug 2022 19:43:19: 22000000 INFO @ Tue, 02 Aug 2022 19:43:22: 19000000 INFO @ Tue, 02 Aug 2022 19:43:28: 21000000 INFO @ Tue, 02 Aug 2022 19:43:34: 23000000 INFO @ Tue, 02 Aug 2022 19:43:37: 20000000 INFO @ Tue, 02 Aug 2022 19:43:42: 22000000 INFO @ Tue, 02 Aug 2022 19:43:49: 24000000 INFO @ Tue, 02 Aug 2022 19:43:51: 21000000 INFO @ Tue, 02 Aug 2022 19:43:57: 23000000 INFO @ Tue, 02 Aug 2022 19:44:04: 25000000 INFO @ Tue, 02 Aug 2022 19:44:05: 22000000 INFO @ Tue, 02 Aug 2022 19:44:13: 24000000 INFO @ Tue, 02 Aug 2022 19:44:18: 23000000 INFO @ Tue, 02 Aug 2022 19:44:20: 26000000 INFO @ Tue, 02 Aug 2022 19:44:28: 25000000 INFO @ Tue, 02 Aug 2022 19:44:32: 24000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 19:44:34: 27000000 INFO @ Tue, 02 Aug 2022 19:44:42: 26000000 INFO @ Tue, 02 Aug 2022 19:44:45: 25000000 INFO @ Tue, 02 Aug 2022 19:44:47: 28000000 INFO @ Tue, 02 Aug 2022 19:44:55: 27000000 INFO @ Tue, 02 Aug 2022 19:44:58: 26000000 INFO @ Tue, 02 Aug 2022 19:45:00: 29000000 INFO @ Tue, 02 Aug 2022 19:45:08: 28000000 INFO @ Tue, 02 Aug 2022 19:45:11: 27000000 INFO @ Tue, 02 Aug 2022 19:45:13: 30000000 INFO @ Tue, 02 Aug 2022 19:45:21: 29000000 INFO @ Tue, 02 Aug 2022 19:45:24: 28000000 INFO @ Tue, 02 Aug 2022 19:45:26: 31000000 INFO @ Tue, 02 Aug 2022 19:45:33: 30000000 INFO @ Tue, 02 Aug 2022 19:45:36: 29000000 INFO @ Tue, 02 Aug 2022 19:45:39: 32000000 INFO @ Tue, 02 Aug 2022 19:45:46: 31000000 INFO @ Tue, 02 Aug 2022 19:45:48: 30000000 INFO @ Tue, 02 Aug 2022 19:45:52: 33000000 INFO @ Tue, 02 Aug 2022 19:46:00: 32000000 INFO @ Tue, 02 Aug 2022 19:46:00: 31000000 INFO @ Tue, 02 Aug 2022 19:46:05: 34000000 INFO @ Tue, 02 Aug 2022 19:46:12: 32000000 INFO @ Tue, 02 Aug 2022 19:46:13: 33000000 INFO @ Tue, 02 Aug 2022 19:46:19: 35000000 INFO @ Tue, 02 Aug 2022 19:46:24: 33000000 INFO @ Tue, 02 Aug 2022 19:46:27: 34000000 INFO @ Tue, 02 Aug 2022 19:46:32: 36000000 INFO @ Tue, 02 Aug 2022 19:46:36: 34000000 INFO @ Tue, 02 Aug 2022 19:46:40: 35000000 INFO @ Tue, 02 Aug 2022 19:46:46: 37000000 INFO @ Tue, 02 Aug 2022 19:46:48: 35000000 INFO @ Tue, 02 Aug 2022 19:46:54: 36000000 INFO @ Tue, 02 Aug 2022 19:46:59: 38000000 INFO @ Tue, 02 Aug 2022 19:47:00: 36000000 INFO @ Tue, 02 Aug 2022 19:47:07: 37000000 INFO @ Tue, 02 Aug 2022 19:47:12: 37000000 INFO @ Tue, 02 Aug 2022 19:47:12: 39000000 INFO @ Tue, 02 Aug 2022 19:47:19: 38000000 INFO @ Tue, 02 Aug 2022 19:47:24: 40000000 INFO @ Tue, 02 Aug 2022 19:47:24: 38000000 INFO @ Tue, 02 Aug 2022 19:47:31: 39000000 INFO @ Tue, 02 Aug 2022 19:47:32: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 19:47:32: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 19:47:32: #1 total tags in treatment: 19077247 INFO @ Tue, 02 Aug 2022 19:47:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 19:47:32: #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 19:47:32: #1 tags after filtering in treatment: 13517564 INFO @ Tue, 02 Aug 2022 19:47:32: #1 Redundant rate of treatment: 0.29 INFO @ Tue, 02 Aug 2022 19:47:32: #1 finished! INFO @ Tue, 02 Aug 2022 19:47:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 19:47:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 19:47:33: #2 number of paired peaks: 1566 INFO @ Tue, 02 Aug 2022 19:47:33: start model_add_line... INFO @ Tue, 02 Aug 2022 19:47:33: start X-correlation... INFO @ Tue, 02 Aug 2022 19:47:33: end of X-cor INFO @ Tue, 02 Aug 2022 19:47:33: #2 finished! INFO @ Tue, 02 Aug 2022 19:47:33: #2 predicted fragment length is 155 bps INFO @ Tue, 02 Aug 2022 19:47:33: #2 alternative fragment length(s) may be 1,155 bps INFO @ Tue, 02 Aug 2022 19:47:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.05_model.r WARNING @ Tue, 02 Aug 2022 19:47:33: #2 Since the d (155) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 19:47:33: #2 You may need to consider one of the other alternative d(s): 1,155 WARNING @ Tue, 02 Aug 2022 19:47:33: #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 19:47:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 19:47:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 19:47:35: 39000000 INFO @ Tue, 02 Aug 2022 19:47:41: 40000000 INFO @ Tue, 02 Aug 2022 19:47:46: 40000000 INFO @ Tue, 02 Aug 2022 19:47:49: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 19:47:49: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 19:47:49: #1 total tags in treatment: 19077247 INFO @ Tue, 02 Aug 2022 19:47:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 19:47:49: #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 19:47:50: #1 tags after filtering in treatment: 13517564 INFO @ Tue, 02 Aug 2022 19:47:50: #1 Redundant rate of treatment: 0.29 INFO @ Tue, 02 Aug 2022 19:47:50: #1 finished! INFO @ Tue, 02 Aug 2022 19:47:50: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 19:47:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 19:47:51: #2 number of paired peaks: 1566 INFO @ Tue, 02 Aug 2022 19:47:51: start model_add_line... INFO @ Tue, 02 Aug 2022 19:47:51: start X-correlation... INFO @ Tue, 02 Aug 2022 19:47:51: end of X-cor INFO @ Tue, 02 Aug 2022 19:47:51: #2 finished! INFO @ Tue, 02 Aug 2022 19:47:51: #2 predicted fragment length is 155 bps INFO @ Tue, 02 Aug 2022 19:47:51: #2 alternative fragment length(s) may be 1,155 bps INFO @ Tue, 02 Aug 2022 19:47:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.10_model.r WARNING @ Tue, 02 Aug 2022 19:47:51: #2 Since the d (155) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 19:47:51: #2 You may need to consider one of the other alternative d(s): 1,155 WARNING @ Tue, 02 Aug 2022 19:47:51: #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 19:47:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 19:47:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 19:47:54: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 19:47:54: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 19:47:54: #1 total tags in treatment: 19077247 INFO @ Tue, 02 Aug 2022 19:47:54: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 19:47:54: #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 19:47:54: #1 tags after filtering in treatment: 13517564 INFO @ Tue, 02 Aug 2022 19:47:54: #1 Redundant rate of treatment: 0.29 INFO @ Tue, 02 Aug 2022 19:47:54: #1 finished! INFO @ Tue, 02 Aug 2022 19:47:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 19:47:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 19:47:55: #2 number of paired peaks: 1566 INFO @ Tue, 02 Aug 2022 19:47:55: start model_add_line... INFO @ Tue, 02 Aug 2022 19:47:56: start X-correlation... INFO @ Tue, 02 Aug 2022 19:47:56: end of X-cor INFO @ Tue, 02 Aug 2022 19:47:56: #2 finished! INFO @ Tue, 02 Aug 2022 19:47:56: #2 predicted fragment length is 155 bps INFO @ Tue, 02 Aug 2022 19:47:56: #2 alternative fragment length(s) may be 1,155 bps INFO @ Tue, 02 Aug 2022 19:47:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.20_model.r WARNING @ Tue, 02 Aug 2022 19:47:56: #2 Since the d (155) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 19:47:56: #2 You may need to consider one of the other alternative d(s): 1,155 WARNING @ Tue, 02 Aug 2022 19:47:56: #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 19:47:56: #3 Call peaks... INFO @ Tue, 02 Aug 2022 19:47:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 19:48:11: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 19:48:28: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 19:48:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.05_peaks.xls INFO @ Tue, 02 Aug 2022 19:48:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 19:48:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.05_summits.bed INFO @ Tue, 02 Aug 2022 19:48:32: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4431 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 19:48:34: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 19:48:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.10_peaks.xls INFO @ Tue, 02 Aug 2022 19:48:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 19:48:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.10_summits.bed INFO @ Tue, 02 Aug 2022 19:48:49: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1580 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 19:48:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.20_peaks.xls INFO @ Tue, 02 Aug 2022 19:48:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 19:48:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10855777/SRX10855777.20_summits.bed INFO @ Tue, 02 Aug 2022 19:48:55: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (488 records, 4 fields): 3 millis CompletedMACS2peakCalling