Job ID = 12265214 SRX = SRX4517988 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16024106 spots for SRR7655592/SRR7655592.sra Written 16024106 spots for SRR7655592/SRR7655592.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265431 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:14:13 16024106 reads; of these: 16024106 (100.00%) were paired; of these: 1812065 (11.31%) aligned concordantly 0 times 13616982 (84.98%) aligned concordantly exactly 1 time 595059 (3.71%) aligned concordantly >1 times ---- 1812065 pairs aligned concordantly 0 times; of these: 920296 (50.79%) aligned discordantly 1 time ---- 891769 pairs aligned 0 times concordantly or discordantly; of these: 1783538 mates make up the pairs; of these: 1392624 (78.08%) aligned 0 times 291724 (16.36%) aligned exactly 1 time 99190 (5.56%) aligned >1 times 95.65% overall alignment rate Time searching: 00:14:14 Overall time: 00:14:14 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 16 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] 874018 / 14939750 = 0.0585 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:43:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.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, 03 Apr 2021 06:43:51: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:43:51: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:43:56: 1000000 INFO @ Sat, 03 Apr 2021 06:44:01: 2000000 INFO @ Sat, 03 Apr 2021 06:44:07: 3000000 INFO @ Sat, 03 Apr 2021 06:44:12: 4000000 INFO @ Sat, 03 Apr 2021 06:44:17: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:44:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.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, 03 Apr 2021 06:44:21: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:44:21: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:44:23: 6000000 INFO @ Sat, 03 Apr 2021 06:44:27: 1000000 INFO @ Sat, 03 Apr 2021 06:44:29: 7000000 INFO @ Sat, 03 Apr 2021 06:44:34: 2000000 INFO @ Sat, 03 Apr 2021 06:44:35: 8000000 INFO @ Sat, 03 Apr 2021 06:44:40: 3000000 INFO @ Sat, 03 Apr 2021 06:44:41: 9000000 INFO @ Sat, 03 Apr 2021 06:44:46: 4000000 INFO @ Sat, 03 Apr 2021 06:44:47: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:44:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.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, 03 Apr 2021 06:44:51: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:44:51: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:44:53: 5000000 INFO @ Sat, 03 Apr 2021 06:44:53: 11000000 INFO @ Sat, 03 Apr 2021 06:44:58: 1000000 INFO @ Sat, 03 Apr 2021 06:44:59: 6000000 INFO @ Sat, 03 Apr 2021 06:44:59: 12000000 INFO @ Sat, 03 Apr 2021 06:45:03: 2000000 INFO @ Sat, 03 Apr 2021 06:45:05: 13000000 INFO @ Sat, 03 Apr 2021 06:45:05: 7000000 INFO @ Sat, 03 Apr 2021 06:45:09: 3000000 INFO @ Sat, 03 Apr 2021 06:45:10: 14000000 INFO @ Sat, 03 Apr 2021 06:45:11: 8000000 INFO @ Sat, 03 Apr 2021 06:45:14: 4000000 INFO @ Sat, 03 Apr 2021 06:45:17: 9000000 INFO @ Sat, 03 Apr 2021 06:45:17: 15000000 INFO @ Sat, 03 Apr 2021 06:45:20: 5000000 INFO @ Sat, 03 Apr 2021 06:45:22: 16000000 INFO @ Sat, 03 Apr 2021 06:45:25: 10000000 INFO @ Sat, 03 Apr 2021 06:45:27: 6000000 INFO @ Sat, 03 Apr 2021 06:45:28: 17000000 INFO @ Sat, 03 Apr 2021 06:45:32: 11000000 INFO @ Sat, 03 Apr 2021 06:45:33: 7000000 INFO @ Sat, 03 Apr 2021 06:45:33: 18000000 INFO @ Sat, 03 Apr 2021 06:45:38: 8000000 INFO @ Sat, 03 Apr 2021 06:45:39: 12000000 INFO @ Sat, 03 Apr 2021 06:45:39: 19000000 INFO @ Sat, 03 Apr 2021 06:45:43: 9000000 INFO @ Sat, 03 Apr 2021 06:45:44: 13000000 INFO @ Sat, 03 Apr 2021 06:45:45: 20000000 INFO @ Sat, 03 Apr 2021 06:45:48: 10000000 INFO @ Sat, 03 Apr 2021 06:45:51: 21000000 INFO @ Sat, 03 Apr 2021 06:45:51: 14000000 INFO @ Sat, 03 Apr 2021 06:45:53: 11000000 INFO @ Sat, 03 Apr 2021 06:45:57: 15000000 INFO @ Sat, 03 Apr 2021 06:45:57: 22000000 INFO @ Sat, 03 Apr 2021 06:45:59: 12000000 INFO @ Sat, 03 Apr 2021 06:46:03: 23000000 INFO @ Sat, 03 Apr 2021 06:46:03: 16000000 INFO @ Sat, 03 Apr 2021 06:46:05: 13000000 INFO @ Sat, 03 Apr 2021 06:46:08: 24000000 INFO @ Sat, 03 Apr 2021 06:46:08: 17000000 INFO @ Sat, 03 Apr 2021 06:46:10: 14000000 INFO @ Sat, 03 Apr 2021 06:46:14: 25000000 INFO @ Sat, 03 Apr 2021 06:46:14: 18000000 INFO @ Sat, 03 Apr 2021 06:46:16: 15000000 INFO @ Sat, 03 Apr 2021 06:46:19: 19000000 INFO @ Sat, 03 Apr 2021 06:46:19: 26000000 INFO @ Sat, 03 Apr 2021 06:46:21: 16000000 INFO @ Sat, 03 Apr 2021 06:46:25: 20000000 INFO @ Sat, 03 Apr 2021 06:46:25: 27000000 INFO @ Sat, 03 Apr 2021 06:46:26: 17000000 INFO @ Sat, 03 Apr 2021 06:46:30: 21000000 INFO @ Sat, 03 Apr 2021 06:46:31: 28000000 INFO @ Sat, 03 Apr 2021 06:46:31: 18000000 INFO @ Sat, 03 Apr 2021 06:46:36: 19000000 INFO @ Sat, 03 Apr 2021 06:46:37: 22000000 INFO @ Sat, 03 Apr 2021 06:46:37: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:46:37: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:46:37: #1 total tags in treatment: 13424969 INFO @ Sat, 03 Apr 2021 06:46:37: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:46:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:46:37: #1 tags after filtering in treatment: 9788004 INFO @ Sat, 03 Apr 2021 06:46:37: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 06:46:37: #1 finished! INFO @ Sat, 03 Apr 2021 06:46:37: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:46:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:46:38: #2 number of paired peaks: 2337 INFO @ Sat, 03 Apr 2021 06:46:38: start model_add_line... INFO @ Sat, 03 Apr 2021 06:46:38: start X-correlation... INFO @ Sat, 03 Apr 2021 06:46:38: end of X-cor INFO @ Sat, 03 Apr 2021 06:46:38: #2 finished! INFO @ Sat, 03 Apr 2021 06:46:38: #2 predicted fragment length is 79 bps INFO @ Sat, 03 Apr 2021 06:46:38: #2 alternative fragment length(s) may be 79 bps INFO @ Sat, 03 Apr 2021 06:46:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.05_model.r WARNING @ Sat, 03 Apr 2021 06:46:38: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:46:38: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Sat, 03 Apr 2021 06:46:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:46:38: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:46:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:46:41: 20000000 INFO @ Sat, 03 Apr 2021 06:46:42: 23000000 INFO @ Sat, 03 Apr 2021 06:46:46: 21000000 INFO @ Sat, 03 Apr 2021 06:46:47: 24000000 INFO @ Sat, 03 Apr 2021 06:46:51: 22000000 INFO @ Sat, 03 Apr 2021 06:46:53: 25000000 INFO @ Sat, 03 Apr 2021 06:46:56: 23000000 INFO @ Sat, 03 Apr 2021 06:46:58: 26000000 INFO @ Sat, 03 Apr 2021 06:47:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:47:01: 24000000 INFO @ Sat, 03 Apr 2021 06:47:03: 27000000 INFO @ Sat, 03 Apr 2021 06:47:06: 25000000 INFO @ Sat, 03 Apr 2021 06:47:09: 28000000 INFO @ Sat, 03 Apr 2021 06:47:11: 26000000 INFO @ Sat, 03 Apr 2021 06:47:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:47:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:47:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.05_summits.bed INFO @ Sat, 03 Apr 2021 06:47:12: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (10503 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:47:14: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:47:14: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:47:14: #1 total tags in treatment: 13424969 INFO @ Sat, 03 Apr 2021 06:47:14: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:47:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:47:15: #1 tags after filtering in treatment: 9788004 INFO @ Sat, 03 Apr 2021 06:47:15: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 06:47:15: #1 finished! INFO @ Sat, 03 Apr 2021 06:47:15: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:47:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:47:16: #2 number of paired peaks: 2337 INFO @ Sat, 03 Apr 2021 06:47:16: start model_add_line... INFO @ Sat, 03 Apr 2021 06:47:16: start X-correlation... INFO @ Sat, 03 Apr 2021 06:47:16: end of X-cor INFO @ Sat, 03 Apr 2021 06:47:16: #2 finished! INFO @ Sat, 03 Apr 2021 06:47:16: #2 predicted fragment length is 79 bps INFO @ Sat, 03 Apr 2021 06:47:16: #2 alternative fragment length(s) may be 79 bps INFO @ Sat, 03 Apr 2021 06:47:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.10_model.r WARNING @ Sat, 03 Apr 2021 06:47:16: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:47:16: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Sat, 03 Apr 2021 06:47:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:47:16: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:47:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:47:16: 27000000 INFO @ Sat, 03 Apr 2021 06:47:22: 28000000 INFO @ Sat, 03 Apr 2021 06:47:26: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:47:26: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:47:26: #1 total tags in treatment: 13424969 INFO @ Sat, 03 Apr 2021 06:47:26: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:47:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:47:27: #1 tags after filtering in treatment: 9788004 INFO @ Sat, 03 Apr 2021 06:47:27: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 06:47:27: #1 finished! INFO @ Sat, 03 Apr 2021 06:47:27: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:47:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:47:27: #2 number of paired peaks: 2337 INFO @ Sat, 03 Apr 2021 06:47:27: start model_add_line... INFO @ Sat, 03 Apr 2021 06:47:28: start X-correlation... INFO @ Sat, 03 Apr 2021 06:47:28: end of X-cor INFO @ Sat, 03 Apr 2021 06:47:28: #2 finished! INFO @ Sat, 03 Apr 2021 06:47:28: #2 predicted fragment length is 79 bps INFO @ Sat, 03 Apr 2021 06:47:28: #2 alternative fragment length(s) may be 79 bps INFO @ Sat, 03 Apr 2021 06:47:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.20_model.r WARNING @ Sat, 03 Apr 2021 06:47:28: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:47:28: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Sat, 03 Apr 2021 06:47:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:47:28: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:47:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:47:35: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:47:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:47:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:47:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.10_summits.bed INFO @ Sat, 03 Apr 2021 06:47:46: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (5431 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:47:48: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:47:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:47:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:47:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4517988/SRX4517988.20_summits.bed INFO @ Sat, 03 Apr 2021 06:47:58: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1519 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。