Job ID = 14168381 SRX = ERX3978742 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 23014096 spots for ERR3975752/ERR3975752.sra Written 23014096 spots for ERR3975752/ERR3975752.sra Read 29016326 spots for ERR3975785/ERR3975785.sra Written 29016326 spots for ERR3975785/ERR3975785.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169771 ("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: 01:05:43 52030422 reads; of these: 52030422 (100.00%) were paired; of these: 24598627 (47.28%) aligned concordantly 0 times 1672280 (3.21%) aligned concordantly exactly 1 time 25759515 (49.51%) aligned concordantly >1 times ---- 24598627 pairs aligned concordantly 0 times; of these: 696743 (2.83%) aligned discordantly 1 time ---- 23901884 pairs aligned 0 times concordantly or discordantly; of these: 47803768 mates make up the pairs; of these: 23049224 (48.22%) aligned 0 times 661700 (1.38%) aligned exactly 1 time 24092844 (50.40%) aligned >1 times 77.85% overall alignment rate Time searching: 01:05:43 Overall time: 01:05:43 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 60 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] 24070481 / 27719296 = 0.8684 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 19:44:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.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 19:44:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:44:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:44:58: 1000000 INFO @ Fri, 10 Dec 2021 19:45:08: 2000000 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 19:45:18: 3000000 INFO @ Fri, 10 Dec 2021 19:45:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.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 19:45:18: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:45:18: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:45:28: 1000000 INFO @ Fri, 10 Dec 2021 19:45:29: 4000000 INFO @ Fri, 10 Dec 2021 19:45:38: 2000000 INFO @ Fri, 10 Dec 2021 19:45:40: 5000000 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 19:45:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.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 19:45:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:45:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:45:49: 3000000 INFO @ Fri, 10 Dec 2021 19:45:51: 6000000 INFO @ Fri, 10 Dec 2021 19:45:58: 1000000 INFO @ Fri, 10 Dec 2021 19:45:59: 4000000 INFO @ Fri, 10 Dec 2021 19:46:02: 7000000 INFO @ Fri, 10 Dec 2021 19:46:09: 2000000 INFO @ Fri, 10 Dec 2021 19:46:09: 5000000 INFO @ Fri, 10 Dec 2021 19:46:13: 8000000 INFO @ Fri, 10 Dec 2021 19:46:19: 6000000 INFO @ Fri, 10 Dec 2021 19:46:19: 3000000 INFO @ Fri, 10 Dec 2021 19:46:24: 9000000 INFO @ Fri, 10 Dec 2021 19:46:28: 7000000 INFO @ Fri, 10 Dec 2021 19:46:29: 4000000 INFO @ Fri, 10 Dec 2021 19:46:35: 10000000 INFO @ Fri, 10 Dec 2021 19:46:38: 8000000 INFO @ Fri, 10 Dec 2021 19:46:39: 5000000 INFO @ Fri, 10 Dec 2021 19:46:46: 11000000 INFO @ Fri, 10 Dec 2021 19:46:49: 9000000 INFO @ Fri, 10 Dec 2021 19:46:49: 6000000 INFO @ Fri, 10 Dec 2021 19:46:57: 12000000 INFO @ Fri, 10 Dec 2021 19:46:59: 10000000 INFO @ Fri, 10 Dec 2021 19:46:59: 7000000 INFO @ Fri, 10 Dec 2021 19:47:08: 13000000 INFO @ Fri, 10 Dec 2021 19:47:09: 11000000 INFO @ Fri, 10 Dec 2021 19:47:09: 8000000 INFO @ Fri, 10 Dec 2021 19:47:19: 12000000 INFO @ Fri, 10 Dec 2021 19:47:20: 14000000 INFO @ Fri, 10 Dec 2021 19:47:20: 9000000 INFO @ Fri, 10 Dec 2021 19:47:29: 13000000 INFO @ Fri, 10 Dec 2021 19:47:30: 10000000 INFO @ Fri, 10 Dec 2021 19:47:31: 15000000 INFO @ Fri, 10 Dec 2021 19:47:39: 14000000 INFO @ Fri, 10 Dec 2021 19:47:40: 11000000 INFO @ Fri, 10 Dec 2021 19:47:42: 16000000 INFO @ Fri, 10 Dec 2021 19:47:49: 15000000 INFO @ Fri, 10 Dec 2021 19:47:50: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:47:53: 17000000 INFO @ Fri, 10 Dec 2021 19:48:00: 16000000 INFO @ Fri, 10 Dec 2021 19:48:00: 13000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 19:48:04: 18000000 INFO @ Fri, 10 Dec 2021 19:48:10: 17000000 INFO @ Fri, 10 Dec 2021 19:48:10: 14000000 INFO @ Fri, 10 Dec 2021 19:48:15: 19000000 INFO @ Fri, 10 Dec 2021 19:48:20: 18000000 INFO @ Fri, 10 Dec 2021 19:48:20: 15000000 INFO @ Fri, 10 Dec 2021 19:48:26: 20000000 INFO @ Fri, 10 Dec 2021 19:48:30: 19000000 INFO @ Fri, 10 Dec 2021 19:48:31: 16000000 INFO @ Fri, 10 Dec 2021 19:48:38: 21000000 INFO @ Fri, 10 Dec 2021 19:48:40: 20000000 INFO @ Fri, 10 Dec 2021 19:48:41: 17000000 INFO @ Fri, 10 Dec 2021 19:48:49: 22000000 INFO @ Fri, 10 Dec 2021 19:48:50: 21000000 INFO @ Fri, 10 Dec 2021 19:48:51: 18000000 INFO @ Fri, 10 Dec 2021 19:49:00: 23000000 INFO @ Fri, 10 Dec 2021 19:49:01: 22000000 INFO @ Fri, 10 Dec 2021 19:49:01: 19000000 INFO @ Fri, 10 Dec 2021 19:49:11: 23000000 INFO @ Fri, 10 Dec 2021 19:49:11: 20000000 INFO @ Fri, 10 Dec 2021 19:49:11: 24000000 INFO @ Fri, 10 Dec 2021 19:49:21: 24000000 INFO @ Fri, 10 Dec 2021 19:49:21: 21000000 INFO @ Fri, 10 Dec 2021 19:49:22: 25000000 INFO @ Fri, 10 Dec 2021 19:49:31: 25000000 INFO @ Fri, 10 Dec 2021 19:49:31: 22000000 INFO @ Fri, 10 Dec 2021 19:49:34: 26000000 INFO @ Fri, 10 Dec 2021 19:49:41: 26000000 INFO @ Fri, 10 Dec 2021 19:49:41: 23000000 INFO @ Fri, 10 Dec 2021 19:49:45: 27000000 INFO @ Fri, 10 Dec 2021 19:49:51: 27000000 INFO @ Fri, 10 Dec 2021 19:49:52: 24000000 INFO @ Fri, 10 Dec 2021 19:49:56: 28000000 INFO @ Fri, 10 Dec 2021 19:50:01: 28000000 INFO @ Fri, 10 Dec 2021 19:50:02: 25000000 INFO @ Fri, 10 Dec 2021 19:50:07: 29000000 INFO @ Fri, 10 Dec 2021 19:50:12: 29000000 INFO @ Fri, 10 Dec 2021 19:50:12: 26000000 INFO @ Fri, 10 Dec 2021 19:50:18: 30000000 INFO @ Fri, 10 Dec 2021 19:50:22: 30000000 INFO @ Fri, 10 Dec 2021 19:50:22: 27000000 INFO @ Fri, 10 Dec 2021 19:50:29: 31000000 INFO @ Fri, 10 Dec 2021 19:50:32: 31000000 INFO @ Fri, 10 Dec 2021 19:50:32: 28000000 INFO @ Fri, 10 Dec 2021 19:50:40: 32000000 INFO @ Fri, 10 Dec 2021 19:50:42: 32000000 INFO @ Fri, 10 Dec 2021 19:50:42: 29000000 INFO @ Fri, 10 Dec 2021 19:50:50: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:50:50: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:50:50: #1 total tags in treatment: 3589973 INFO @ Fri, 10 Dec 2021 19:50:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:50:50: #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 19:50:50: #1 tags after filtering in treatment: 1839503 INFO @ Fri, 10 Dec 2021 19:50:50: #1 Redundant rate of treatment: 0.49 INFO @ Fri, 10 Dec 2021 19:50:50: #1 finished! INFO @ Fri, 10 Dec 2021 19:50:50: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:50:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:50:50: #2 number of paired peaks: 4302 INFO @ Fri, 10 Dec 2021 19:50:50: start model_add_line... INFO @ Fri, 10 Dec 2021 19:50:50: start X-correlation... INFO @ Fri, 10 Dec 2021 19:50:50: end of X-cor INFO @ Fri, 10 Dec 2021 19:50:50: #2 finished! INFO @ Fri, 10 Dec 2021 19:50:50: #2 predicted fragment length is 216 bps INFO @ Fri, 10 Dec 2021 19:50:50: #2 alternative fragment length(s) may be 216 bps INFO @ Fri, 10 Dec 2021 19:50:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.05_model.r WARNING @ Fri, 10 Dec 2021 19:50:50: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:50:50: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Fri, 10 Dec 2021 19:50:50: #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 19:50:50: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:50:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:50:51: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:50:51: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:50:51: #1 total tags in treatment: 3589973 INFO @ Fri, 10 Dec 2021 19:50:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:50:51: #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 19:50:51: #1 tags after filtering in treatment: 1839503 INFO @ Fri, 10 Dec 2021 19:50:51: #1 Redundant rate of treatment: 0.49 INFO @ Fri, 10 Dec 2021 19:50:51: #1 finished! INFO @ Fri, 10 Dec 2021 19:50:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:50:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:50:51: #2 number of paired peaks: 4302 INFO @ Fri, 10 Dec 2021 19:50:51: start model_add_line... INFO @ Fri, 10 Dec 2021 19:50:51: start X-correlation... INFO @ Fri, 10 Dec 2021 19:50:51: end of X-cor INFO @ Fri, 10 Dec 2021 19:50:51: #2 finished! INFO @ Fri, 10 Dec 2021 19:50:51: #2 predicted fragment length is 216 bps INFO @ Fri, 10 Dec 2021 19:50:51: #2 alternative fragment length(s) may be 216 bps INFO @ Fri, 10 Dec 2021 19:50:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.10_model.r WARNING @ Fri, 10 Dec 2021 19:50:51: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:50:51: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Fri, 10 Dec 2021 19:50:51: #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 19:50:51: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:50:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:50:52: 30000000 INFO @ Fri, 10 Dec 2021 19:50:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:50:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:50:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:50:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:50:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.05_summits.bed INFO @ Fri, 10 Dec 2021 19:50:57: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4116 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:50:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:50:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:50:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.10_summits.bed INFO @ Fri, 10 Dec 2021 19:50:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1792 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:51:00: 31000000 INFO @ Fri, 10 Dec 2021 19:51:08: 32000000 INFO @ Fri, 10 Dec 2021 19:51:16: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:51:16: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:51:16: #1 total tags in treatment: 3589973 INFO @ Fri, 10 Dec 2021 19:51:16: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:51:16: #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 19:51:16: #1 tags after filtering in treatment: 1839503 INFO @ Fri, 10 Dec 2021 19:51:16: #1 Redundant rate of treatment: 0.49 INFO @ Fri, 10 Dec 2021 19:51:16: #1 finished! INFO @ Fri, 10 Dec 2021 19:51:16: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:51:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:51:16: #2 number of paired peaks: 4302 INFO @ Fri, 10 Dec 2021 19:51:16: start model_add_line... INFO @ Fri, 10 Dec 2021 19:51:16: start X-correlation... INFO @ Fri, 10 Dec 2021 19:51:16: end of X-cor INFO @ Fri, 10 Dec 2021 19:51:16: #2 finished! INFO @ Fri, 10 Dec 2021 19:51:16: #2 predicted fragment length is 216 bps INFO @ Fri, 10 Dec 2021 19:51:16: #2 alternative fragment length(s) may be 216 bps INFO @ Fri, 10 Dec 2021 19:51:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.20_model.r WARNING @ Fri, 10 Dec 2021 19:51:16: #2 Since the d (216) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:51:16: #2 You may need to consider one of the other alternative d(s): 216 WARNING @ Fri, 10 Dec 2021 19:51:16: #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 19:51:16: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:51:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:51:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:51:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:51:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:51:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978742/ERX3978742.20_summits.bed INFO @ Fri, 10 Dec 2021 19:51:23: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (519 records, 4 fields): 1 millis CompletedMACS2peakCalling