Job ID = 14171835 SRX = SRX9008841 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14801303 spots for SRR12518313/SRR12518313.sra Written 14801303 spots for SRR12518313/SRR12518313.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172408 ("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: 00:27:48 14801303 reads; of these: 14801303 (100.00%) were paired; of these: 2490148 (16.82%) aligned concordantly 0 times 10277353 (69.44%) aligned concordantly exactly 1 time 2033802 (13.74%) aligned concordantly >1 times ---- 2490148 pairs aligned concordantly 0 times; of these: 1330484 (53.43%) aligned discordantly 1 time ---- 1159664 pairs aligned 0 times concordantly or discordantly; of these: 2319328 mates make up the pairs; of these: 1491223 (64.30%) aligned 0 times 352048 (15.18%) aligned exactly 1 time 476057 (20.53%) aligned >1 times 94.96% overall alignment rate Time searching: 00:27:49 Overall time: 00:27:49 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 12 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] 775655 / 13550674 = 0.0572 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 13:41:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.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 13:41:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:41:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:41:46: 1000000 INFO @ Sat, 11 Dec 2021 13:41:53: 2000000 INFO @ Sat, 11 Dec 2021 13:42:01: 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 13:42:08: 4000000 INFO @ Sat, 11 Dec 2021 13:42:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.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 13:42:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:42:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:42:17: 1000000 INFO @ Sat, 11 Dec 2021 13:42:18: 5000000 INFO @ Sat, 11 Dec 2021 13:42:26: 6000000 INFO @ Sat, 11 Dec 2021 13:42:26: 2000000 INFO @ Sat, 11 Dec 2021 13:42:34: 7000000 INFO @ Sat, 11 Dec 2021 13:42:35: 3000000 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 13:42:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.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 13:42:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 13:42:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 13:42:42: 8000000 INFO @ Sat, 11 Dec 2021 13:42:43: 4000000 INFO @ Sat, 11 Dec 2021 13:42:47: 1000000 INFO @ Sat, 11 Dec 2021 13:42:49: 9000000 INFO @ Sat, 11 Dec 2021 13:42:51: 5000000 INFO @ Sat, 11 Dec 2021 13:42:55: 2000000 INFO @ Sat, 11 Dec 2021 13:42:57: 10000000 INFO @ Sat, 11 Dec 2021 13:42:59: 6000000 INFO @ Sat, 11 Dec 2021 13:43:03: 3000000 INFO @ Sat, 11 Dec 2021 13:43:05: 11000000 INFO @ Sat, 11 Dec 2021 13:43:08: 7000000 INFO @ Sat, 11 Dec 2021 13:43:11: 4000000 INFO @ Sat, 11 Dec 2021 13:43:12: 12000000 INFO @ Sat, 11 Dec 2021 13:43:17: 8000000 INFO @ Sat, 11 Dec 2021 13:43:19: 5000000 INFO @ Sat, 11 Dec 2021 13:43:20: 13000000 INFO @ Sat, 11 Dec 2021 13:43:26: 9000000 INFO @ Sat, 11 Dec 2021 13:43:27: 6000000 INFO @ Sat, 11 Dec 2021 13:43:28: 14000000 INFO @ Sat, 11 Dec 2021 13:43:34: 10000000 INFO @ Sat, 11 Dec 2021 13:43:35: 15000000 INFO @ Sat, 11 Dec 2021 13:43:35: 7000000 INFO @ Sat, 11 Dec 2021 13:43:43: 16000000 INFO @ Sat, 11 Dec 2021 13:43:43: 11000000 INFO @ Sat, 11 Dec 2021 13:43:44: 8000000 INFO @ Sat, 11 Dec 2021 13:43:50: 17000000 INFO @ Sat, 11 Dec 2021 13:43:52: 12000000 INFO @ Sat, 11 Dec 2021 13:43:53: 9000000 INFO @ Sat, 11 Dec 2021 13:43:59: 18000000 INFO @ Sat, 11 Dec 2021 13:44:01: 13000000 INFO @ Sat, 11 Dec 2021 13:44:02: 10000000 INFO @ Sat, 11 Dec 2021 13:44:09: 19000000 INFO @ Sat, 11 Dec 2021 13:44:10: 14000000 INFO @ Sat, 11 Dec 2021 13:44:11: 11000000 INFO @ Sat, 11 Dec 2021 13:44:18: 20000000 INFO @ Sat, 11 Dec 2021 13:44:18: 15000000 INFO @ Sat, 11 Dec 2021 13:44:19: 12000000 INFO @ Sat, 11 Dec 2021 13:44:27: 16000000 INFO @ Sat, 11 Dec 2021 13:44:27: 21000000 INFO @ Sat, 11 Dec 2021 13:44:28: 13000000 INFO @ Sat, 11 Dec 2021 13:44:36: 17000000 INFO @ Sat, 11 Dec 2021 13:44:36: 22000000 INFO @ Sat, 11 Dec 2021 13:44:37: 14000000 INFO @ Sat, 11 Dec 2021 13:44:43: 18000000 INFO @ Sat, 11 Dec 2021 13:44:45: 15000000 INFO @ Sat, 11 Dec 2021 13:44:45: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 13:44:51: 19000000 INFO @ Sat, 11 Dec 2021 13:44:54: 16000000 INFO @ Sat, 11 Dec 2021 13:44:54: 24000000 INFO @ Sat, 11 Dec 2021 13:44:59: 20000000 INFO @ Sat, 11 Dec 2021 13:45:02: 17000000 INFO @ Sat, 11 Dec 2021 13:45:04: 25000000 INFO @ Sat, 11 Dec 2021 13:45:06: 21000000 INFO @ Sat, 11 Dec 2021 13:45:10: 18000000 INFO @ Sat, 11 Dec 2021 13:45:13: 26000000 INFO @ Sat, 11 Dec 2021 13:45:14: 22000000 INFO @ Sat, 11 Dec 2021 13:45:17: 19000000 INFO @ Sat, 11 Dec 2021 13:45:18: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:45:18: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:45:18: #1 total tags in treatment: 11610343 INFO @ Sat, 11 Dec 2021 13:45:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:45:18: #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 13:45:18: #1 tags after filtering in treatment: 11227126 INFO @ Sat, 11 Dec 2021 13:45:18: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 13:45:18: #1 finished! INFO @ Sat, 11 Dec 2021 13:45:18: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:45:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:45:19: #2 number of paired peaks: 144 WARNING @ Sat, 11 Dec 2021 13:45:19: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Sat, 11 Dec 2021 13:45:19: start model_add_line... INFO @ Sat, 11 Dec 2021 13:45:19: start X-correlation... INFO @ Sat, 11 Dec 2021 13:45:19: end of X-cor INFO @ Sat, 11 Dec 2021 13:45:19: #2 finished! INFO @ Sat, 11 Dec 2021 13:45:19: #2 predicted fragment length is 205 bps INFO @ Sat, 11 Dec 2021 13:45:19: #2 alternative fragment length(s) may be 3,177,182,205,582,590 bps INFO @ Sat, 11 Dec 2021 13:45:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.05_model.r INFO @ Sat, 11 Dec 2021 13:45:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:45:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:45:21: 23000000 INFO @ Sat, 11 Dec 2021 13:45:24: 20000000 INFO @ Sat, 11 Dec 2021 13:45:29: 24000000 INFO @ Sat, 11 Dec 2021 13:45:31: 21000000 INFO @ Sat, 11 Dec 2021 13:45:36: 25000000 INFO @ Sat, 11 Dec 2021 13:45:38: 22000000 INFO @ Sat, 11 Dec 2021 13:45:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:45:43: 26000000 INFO @ Sat, 11 Dec 2021 13:45:45: 23000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 13:45:47: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:45:47: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:45:47: #1 total tags in treatment: 11610343 INFO @ Sat, 11 Dec 2021 13:45:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:45:47: #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 13:45:47: #1 tags after filtering in treatment: 11227126 INFO @ Sat, 11 Dec 2021 13:45:47: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 13:45:47: #1 finished! INFO @ Sat, 11 Dec 2021 13:45:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:45:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:45:48: #2 number of paired peaks: 144 WARNING @ Sat, 11 Dec 2021 13:45:48: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Sat, 11 Dec 2021 13:45:48: start model_add_line... INFO @ Sat, 11 Dec 2021 13:45:48: start X-correlation... INFO @ Sat, 11 Dec 2021 13:45:48: end of X-cor INFO @ Sat, 11 Dec 2021 13:45:48: #2 finished! INFO @ Sat, 11 Dec 2021 13:45:48: #2 predicted fragment length is 205 bps INFO @ Sat, 11 Dec 2021 13:45:48: #2 alternative fragment length(s) may be 3,177,182,205,582,590 bps INFO @ Sat, 11 Dec 2021 13:45:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.10_model.r INFO @ Sat, 11 Dec 2021 13:45:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:45:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:45:51: 24000000 INFO @ Sat, 11 Dec 2021 13:45:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.05_peaks.xls INFO @ Sat, 11 Dec 2021 13:45:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:45:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.05_summits.bed INFO @ Sat, 11 Dec 2021 13:45:52: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (417 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:45:57: 25000000 INFO @ Sat, 11 Dec 2021 13:46:03: 26000000 INFO @ Sat, 11 Dec 2021 13:46:06: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 13:46:06: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 13:46:06: #1 total tags in treatment: 11610343 INFO @ Sat, 11 Dec 2021 13:46:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 13:46:06: #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 13:46:06: #1 tags after filtering in treatment: 11227126 INFO @ Sat, 11 Dec 2021 13:46:06: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 11 Dec 2021 13:46:06: #1 finished! INFO @ Sat, 11 Dec 2021 13:46:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 13:46:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 13:46:07: #2 number of paired peaks: 144 WARNING @ Sat, 11 Dec 2021 13:46:07: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Sat, 11 Dec 2021 13:46:07: start model_add_line... INFO @ Sat, 11 Dec 2021 13:46:07: start X-correlation... INFO @ Sat, 11 Dec 2021 13:46:07: end of X-cor INFO @ Sat, 11 Dec 2021 13:46:07: #2 finished! INFO @ Sat, 11 Dec 2021 13:46:07: #2 predicted fragment length is 205 bps INFO @ Sat, 11 Dec 2021 13:46:07: #2 alternative fragment length(s) may be 3,177,182,205,582,590 bps INFO @ Sat, 11 Dec 2021 13:46:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.20_model.r INFO @ Sat, 11 Dec 2021 13:46:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 13:46:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 13:46:10: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:46:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.10_peaks.xls INFO @ Sat, 11 Dec 2021 13:46:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:46:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.10_summits.bed INFO @ Sat, 11 Dec 2021 13:46:21: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (145 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 13:46:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 13:46:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.20_peaks.xls INFO @ Sat, 11 Dec 2021 13:46:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 13:46:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9008841/SRX9008841.20_summits.bed INFO @ Sat, 11 Dec 2021 13:46:40: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (53 records, 4 fields): 1 millis CompletedMACS2peakCalling