Job ID = 14167961 SRX = ERX3978807 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 26022657 spots for ERR3975846/ERR3975846.sra Written 26022657 spots for ERR3975846/ERR3975846.sra Read 20485225 spots for ERR3975875/ERR3975875.sra Written 20485225 spots for ERR3975875/ERR3975875.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168860 ("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: 01:19:28 46507882 reads; of these: 46507882 (100.00%) were paired; of these: 12569864 (27.03%) aligned concordantly 0 times 26059424 (56.03%) aligned concordantly exactly 1 time 7878594 (16.94%) aligned concordantly >1 times ---- 12569864 pairs aligned concordantly 0 times; of these: 2127002 (16.92%) aligned discordantly 1 time ---- 10442862 pairs aligned 0 times concordantly or discordantly; of these: 20885724 mates make up the pairs; of these: 18846810 (90.24%) aligned 0 times 727257 (3.48%) aligned exactly 1 time 1311657 (6.28%) aligned >1 times 79.74% overall alignment rate Time searching: 01:19:29 Overall time: 01:19:29 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 44 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] 18919427 / 35868777 = 0.5275 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 @ Fri, 10 Dec 2021 15:41:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.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 @ Fri, 10 Dec 2021 15:41:17: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:41:17: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:41:25: 1000000 INFO @ Fri, 10 Dec 2021 15:41:31: 2000000 INFO @ Fri, 10 Dec 2021 15:41:38: 3000000 INFO @ Fri, 10 Dec 2021 15:41:44: 4000000 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 @ Fri, 10 Dec 2021 15:41:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.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 @ Fri, 10 Dec 2021 15:41:47: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:41:47: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:41:51: 5000000 INFO @ Fri, 10 Dec 2021 15:41:55: 1000000 INFO @ Fri, 10 Dec 2021 15:41:58: 6000000 INFO @ Fri, 10 Dec 2021 15:42:02: 2000000 INFO @ Fri, 10 Dec 2021 15:42:05: 7000000 INFO @ Fri, 10 Dec 2021 15:42:10: 3000000 INFO @ Fri, 10 Dec 2021 15:42:13: 8000000 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 @ Fri, 10 Dec 2021 15:42:17: 4000000 INFO @ Fri, 10 Dec 2021 15:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.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 @ Fri, 10 Dec 2021 15:42:17: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:42:17: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:42:20: 9000000 INFO @ Fri, 10 Dec 2021 15:42:25: 5000000 INFO @ Fri, 10 Dec 2021 15:42:26: 1000000 INFO @ Fri, 10 Dec 2021 15:42:27: 10000000 INFO @ Fri, 10 Dec 2021 15:42:32: 6000000 INFO @ Fri, 10 Dec 2021 15:42:33: 2000000 INFO @ Fri, 10 Dec 2021 15:42:35: 11000000 INFO @ Fri, 10 Dec 2021 15:42:40: 7000000 INFO @ Fri, 10 Dec 2021 15:42:41: 3000000 INFO @ Fri, 10 Dec 2021 15:42:42: 12000000 INFO @ Fri, 10 Dec 2021 15:42:47: 8000000 INFO @ Fri, 10 Dec 2021 15:42:49: 4000000 INFO @ Fri, 10 Dec 2021 15:42:50: 13000000 INFO @ Fri, 10 Dec 2021 15:42:54: 9000000 INFO @ Fri, 10 Dec 2021 15:42:56: 5000000 INFO @ Fri, 10 Dec 2021 15:42:57: 14000000 INFO @ Fri, 10 Dec 2021 15:43:02: 10000000 INFO @ Fri, 10 Dec 2021 15:43:04: 6000000 INFO @ Fri, 10 Dec 2021 15:43:05: 15000000 INFO @ Fri, 10 Dec 2021 15:43:09: 11000000 INFO @ Fri, 10 Dec 2021 15:43:12: 7000000 INFO @ Fri, 10 Dec 2021 15:43:12: 16000000 INFO @ Fri, 10 Dec 2021 15:43:16: 12000000 INFO @ Fri, 10 Dec 2021 15:43:19: 8000000 INFO @ Fri, 10 Dec 2021 15:43:20: 17000000 INFO @ Fri, 10 Dec 2021 15:43:24: 13000000 INFO @ Fri, 10 Dec 2021 15:43:26: 9000000 INFO @ Fri, 10 Dec 2021 15:43:27: 18000000 INFO @ Fri, 10 Dec 2021 15:43:31: 14000000 INFO @ Fri, 10 Dec 2021 15:43:34: 10000000 INFO @ Fri, 10 Dec 2021 15:43:34: 19000000 INFO @ Fri, 10 Dec 2021 15:43:38: 15000000 INFO @ Fri, 10 Dec 2021 15:43:41: 11000000 INFO @ Fri, 10 Dec 2021 15:43:41: 20000000 INFO @ Fri, 10 Dec 2021 15:43:45: 16000000 INFO @ Fri, 10 Dec 2021 15:43:48: 12000000 INFO @ Fri, 10 Dec 2021 15:43:48: 21000000 INFO @ Fri, 10 Dec 2021 15:43:52: 17000000 INFO @ Fri, 10 Dec 2021 15:43:55: 13000000 INFO @ Fri, 10 Dec 2021 15:43:56: 22000000 INFO @ Fri, 10 Dec 2021 15:43:59: 18000000 INFO @ Fri, 10 Dec 2021 15:44:03: 14000000 INFO @ Fri, 10 Dec 2021 15:44:03: 23000000 INFO @ Fri, 10 Dec 2021 15:44:06: 19000000 INFO @ Fri, 10 Dec 2021 15:44:10: 15000000 INFO @ Fri, 10 Dec 2021 15:44:10: 24000000 INFO @ Fri, 10 Dec 2021 15:44:13: 20000000 INFO @ Fri, 10 Dec 2021 15:44:17: 16000000 INFO @ Fri, 10 Dec 2021 15:44:17: 25000000 INFO @ Fri, 10 Dec 2021 15:44:21: 21000000 INFO @ Fri, 10 Dec 2021 15:44:24: 17000000 INFO @ Fri, 10 Dec 2021 15:44:24: 26000000 INFO @ Fri, 10 Dec 2021 15:44:28: 22000000 INFO @ Fri, 10 Dec 2021 15:44:31: 18000000 INFO @ Fri, 10 Dec 2021 15:44:31: 27000000 INFO @ Fri, 10 Dec 2021 15:44:35: 23000000 INFO @ Fri, 10 Dec 2021 15:44:38: 19000000 INFO @ Fri, 10 Dec 2021 15:44:38: 28000000 INFO @ Fri, 10 Dec 2021 15:44:42: 24000000 INFO @ Fri, 10 Dec 2021 15:44:45: 20000000 INFO @ Fri, 10 Dec 2021 15:44:45: 29000000 INFO @ Fri, 10 Dec 2021 15:44:49: 25000000 INFO @ Fri, 10 Dec 2021 15:44:52: 21000000 INFO @ Fri, 10 Dec 2021 15:44:53: 30000000 INFO @ Fri, 10 Dec 2021 15:44:56: 26000000 INFO @ Fri, 10 Dec 2021 15:44:59: 22000000 INFO @ Fri, 10 Dec 2021 15:45:00: 31000000 INFO @ Fri, 10 Dec 2021 15:45:03: 27000000 INFO @ Fri, 10 Dec 2021 15:45:07: 23000000 INFO @ Fri, 10 Dec 2021 15:45:07: 32000000 INFO @ Fri, 10 Dec 2021 15:45:10: 28000000 INFO @ Fri, 10 Dec 2021 15:45:14: 24000000 INFO @ Fri, 10 Dec 2021 15:45:14: 33000000 INFO @ Fri, 10 Dec 2021 15:45:17: 29000000 INFO @ Fri, 10 Dec 2021 15:45:21: 25000000 INFO @ Fri, 10 Dec 2021 15:45:21: 34000000 INFO @ Fri, 10 Dec 2021 15:45:24: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 15:45:28: 26000000 INFO @ Fri, 10 Dec 2021 15:45:28: 35000000 INFO @ Fri, 10 Dec 2021 15:45:31: 31000000 INFO @ Fri, 10 Dec 2021 15:45:35: 27000000 INFO @ Fri, 10 Dec 2021 15:45:36: 36000000 INFO @ Fri, 10 Dec 2021 15:45:39: #1 tag size is determined as 119 bps INFO @ Fri, 10 Dec 2021 15:45:39: #1 tag size = 119 INFO @ Fri, 10 Dec 2021 15:45:39: #1 total tags in treatment: 15776191 INFO @ Fri, 10 Dec 2021 15:45:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:45:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:45:39: 32000000 INFO @ Fri, 10 Dec 2021 15:45:39: #1 tags after filtering in treatment: 11623914 INFO @ Fri, 10 Dec 2021 15:45:39: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 10 Dec 2021 15:45:39: #1 finished! INFO @ Fri, 10 Dec 2021 15:45:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:45:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:45:40: #2 number of paired peaks: 3903 INFO @ Fri, 10 Dec 2021 15:45:40: start model_add_line... INFO @ Fri, 10 Dec 2021 15:45:40: start X-correlation... INFO @ Fri, 10 Dec 2021 15:45:40: end of X-cor INFO @ Fri, 10 Dec 2021 15:45:40: #2 finished! INFO @ Fri, 10 Dec 2021 15:45:40: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Dec 2021 15:45:40: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Dec 2021 15:45:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.05_model.r WARNING @ Fri, 10 Dec 2021 15:45:40: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:45:40: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Fri, 10 Dec 2021 15:45:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 15:45:40: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:45:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:45:42: 28000000 INFO @ Fri, 10 Dec 2021 15:45:46: 33000000 INFO @ Fri, 10 Dec 2021 15:45:49: 29000000 INFO @ Fri, 10 Dec 2021 15:45:53: 34000000 INFO @ Fri, 10 Dec 2021 15:45:57: 30000000 INFO @ Fri, 10 Dec 2021 15:46:00: 35000000 INFO @ Fri, 10 Dec 2021 15:46:04: 31000000 INFO @ Fri, 10 Dec 2021 15:46:08: 36000000 INFO @ Fri, 10 Dec 2021 15:46:08: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:46:10: #1 tag size is determined as 119 bps INFO @ Fri, 10 Dec 2021 15:46:10: #1 tag size = 119 INFO @ Fri, 10 Dec 2021 15:46:10: #1 total tags in treatment: 15776191 INFO @ Fri, 10 Dec 2021 15:46:10: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:46:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:46:10: #1 tags after filtering in treatment: 11623914 INFO @ Fri, 10 Dec 2021 15:46:10: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 10 Dec 2021 15:46:10: #1 finished! INFO @ Fri, 10 Dec 2021 15:46:10: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:46:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:46:11: 32000000 INFO @ Fri, 10 Dec 2021 15:46:12: #2 number of paired peaks: 3903 INFO @ Fri, 10 Dec 2021 15:46:12: start model_add_line... INFO @ Fri, 10 Dec 2021 15:46:12: start X-correlation... INFO @ Fri, 10 Dec 2021 15:46:12: end of X-cor INFO @ Fri, 10 Dec 2021 15:46:12: #2 finished! INFO @ Fri, 10 Dec 2021 15:46:12: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Dec 2021 15:46:12: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Dec 2021 15:46:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.10_model.r WARNING @ Fri, 10 Dec 2021 15:46:12: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:46:12: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Fri, 10 Dec 2021 15:46:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 15:46:12: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:46:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:46:17: 33000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 15:46:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.05_peaks.xls INFO @ Fri, 10 Dec 2021 15:46:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:46:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.05_summits.bed INFO @ Fri, 10 Dec 2021 15:46:22: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (14522 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:46:24: 34000000 INFO @ Fri, 10 Dec 2021 15:46:30: 35000000 INFO @ Fri, 10 Dec 2021 15:46:37: 36000000 INFO @ Fri, 10 Dec 2021 15:46:39: #1 tag size is determined as 119 bps INFO @ Fri, 10 Dec 2021 15:46:39: #1 tag size = 119 INFO @ Fri, 10 Dec 2021 15:46:39: #1 total tags in treatment: 15776191 INFO @ Fri, 10 Dec 2021 15:46:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:46:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:46:39: #1 tags after filtering in treatment: 11623914 INFO @ Fri, 10 Dec 2021 15:46:39: #1 Redundant rate of treatment: 0.26 INFO @ Fri, 10 Dec 2021 15:46:39: #1 finished! INFO @ Fri, 10 Dec 2021 15:46:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:46:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:46:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:46:40: #2 number of paired peaks: 3903 INFO @ Fri, 10 Dec 2021 15:46:40: start model_add_line... INFO @ Fri, 10 Dec 2021 15:46:40: start X-correlation... INFO @ Fri, 10 Dec 2021 15:46:40: end of X-cor INFO @ Fri, 10 Dec 2021 15:46:40: #2 finished! INFO @ Fri, 10 Dec 2021 15:46:40: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Dec 2021 15:46:40: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Dec 2021 15:46:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.20_model.r WARNING @ Fri, 10 Dec 2021 15:46:40: #2 Since the d (156) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:46:40: #2 You may need to consider one of the other alternative d(s): 156 WARNING @ Fri, 10 Dec 2021 15:46:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 15:46:40: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:46:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:46:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.10_peaks.xls INFO @ Fri, 10 Dec 2021 15:46:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:46:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.10_summits.bed INFO @ Fri, 10 Dec 2021 15:46:53: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10850 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:47:08: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:47:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.20_peaks.xls INFO @ Fri, 10 Dec 2021 15:47:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:47:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978807/ERX3978807.20_summits.bed INFO @ Fri, 10 Dec 2021 15:47:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6640 records, 4 fields): 7 millis CompletedMACS2peakCalling