Job ID = 12265217 SRX = SRX4517990 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16977532 spots for SRR7655594/SRR7655594.sra Written 16977532 spots for SRR7655594/SRR7655594.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265429 ("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: 00:13:24 16977532 reads; of these: 16977532 (100.00%) were paired; of these: 1468714 (8.65%) aligned concordantly 0 times 14829822 (87.35%) aligned concordantly exactly 1 time 678996 (4.00%) aligned concordantly >1 times ---- 1468714 pairs aligned concordantly 0 times; of these: 670613 (45.66%) aligned discordantly 1 time ---- 798101 pairs aligned 0 times concordantly or discordantly; of these: 1596202 mates make up the pairs; of these: 1237236 (77.51%) aligned 0 times 275167 (17.24%) aligned exactly 1 time 83799 (5.25%) aligned >1 times 96.36% overall alignment rate Time searching: 00:13:24 Overall time: 00:13:24 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] 862529 / 16036945 = 0.0538 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 06:42:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.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 06:42:35: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:42:35: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:42:40: 1000000 INFO @ Sat, 03 Apr 2021 06:42:45: 2000000 INFO @ Sat, 03 Apr 2021 06:42:51: 3000000 INFO @ Sat, 03 Apr 2021 06:42:56: 4000000 INFO @ Sat, 03 Apr 2021 06:43:01: 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 06:43:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.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 06:43:05: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:43:05: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:43:07: 6000000 INFO @ Sat, 03 Apr 2021 06:43:10: 1000000 INFO @ Sat, 03 Apr 2021 06:43:12: 7000000 INFO @ Sat, 03 Apr 2021 06:43:16: 2000000 INFO @ Sat, 03 Apr 2021 06:43:18: 8000000 INFO @ Sat, 03 Apr 2021 06:43:21: 3000000 INFO @ Sat, 03 Apr 2021 06:43:23: 9000000 INFO @ Sat, 03 Apr 2021 06:43:27: 4000000 INFO @ Sat, 03 Apr 2021 06:43:29: 10000000 INFO @ Sat, 03 Apr 2021 06:43:32: 5000000 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 06:43:34: 11000000 INFO @ Sat, 03 Apr 2021 06:43:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.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 06:43:35: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:43:35: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:43:38: 6000000 INFO @ Sat, 03 Apr 2021 06:43:40: 12000000 INFO @ Sat, 03 Apr 2021 06:43:41: 1000000 INFO @ Sat, 03 Apr 2021 06:43:43: 7000000 INFO @ Sat, 03 Apr 2021 06:43:46: 13000000 INFO @ Sat, 03 Apr 2021 06:43:47: 2000000 INFO @ Sat, 03 Apr 2021 06:43:48: 8000000 INFO @ Sat, 03 Apr 2021 06:43:53: 14000000 INFO @ Sat, 03 Apr 2021 06:43:54: 9000000 INFO @ Sat, 03 Apr 2021 06:43:54: 3000000 INFO @ Sat, 03 Apr 2021 06:43:59: 15000000 INFO @ Sat, 03 Apr 2021 06:43:59: 10000000 INFO @ Sat, 03 Apr 2021 06:44:00: 4000000 INFO @ Sat, 03 Apr 2021 06:44:05: 11000000 INFO @ Sat, 03 Apr 2021 06:44:05: 16000000 INFO @ Sat, 03 Apr 2021 06:44:07: 5000000 INFO @ Sat, 03 Apr 2021 06:44:10: 12000000 INFO @ Sat, 03 Apr 2021 06:44:12: 17000000 INFO @ Sat, 03 Apr 2021 06:44:13: 6000000 INFO @ Sat, 03 Apr 2021 06:44:16: 13000000 INFO @ Sat, 03 Apr 2021 06:44:18: 18000000 INFO @ Sat, 03 Apr 2021 06:44:19: 7000000 INFO @ Sat, 03 Apr 2021 06:44:21: 14000000 INFO @ Sat, 03 Apr 2021 06:44:24: 19000000 INFO @ Sat, 03 Apr 2021 06:44:25: 8000000 INFO @ Sat, 03 Apr 2021 06:44:26: 15000000 INFO @ Sat, 03 Apr 2021 06:44:31: 20000000 INFO @ Sat, 03 Apr 2021 06:44:31: 16000000 INFO @ Sat, 03 Apr 2021 06:44:32: 9000000 INFO @ Sat, 03 Apr 2021 06:44:37: 17000000 INFO @ Sat, 03 Apr 2021 06:44:37: 21000000 INFO @ Sat, 03 Apr 2021 06:44:38: 10000000 INFO @ Sat, 03 Apr 2021 06:44:42: 18000000 INFO @ Sat, 03 Apr 2021 06:44:43: 22000000 INFO @ Sat, 03 Apr 2021 06:44:44: 11000000 INFO @ Sat, 03 Apr 2021 06:44:48: 19000000 INFO @ Sat, 03 Apr 2021 06:44:49: 23000000 INFO @ Sat, 03 Apr 2021 06:44:50: 12000000 INFO @ Sat, 03 Apr 2021 06:44:53: 20000000 INFO @ Sat, 03 Apr 2021 06:44:55: 24000000 INFO @ Sat, 03 Apr 2021 06:44:56: 13000000 INFO @ Sat, 03 Apr 2021 06:44:59: 21000000 INFO @ Sat, 03 Apr 2021 06:45:01: 25000000 INFO @ Sat, 03 Apr 2021 06:45:02: 14000000 INFO @ Sat, 03 Apr 2021 06:45:04: 22000000 INFO @ Sat, 03 Apr 2021 06:45:07: 26000000 INFO @ Sat, 03 Apr 2021 06:45:08: 15000000 INFO @ Sat, 03 Apr 2021 06:45:09: 23000000 INFO @ Sat, 03 Apr 2021 06:45:13: 27000000 INFO @ Sat, 03 Apr 2021 06:45:14: 24000000 INFO @ Sat, 03 Apr 2021 06:45:15: 16000000 INFO @ Sat, 03 Apr 2021 06:45:19: 28000000 INFO @ Sat, 03 Apr 2021 06:45:19: 25000000 INFO @ Sat, 03 Apr 2021 06:45:22: 17000000 INFO @ Sat, 03 Apr 2021 06:45:25: 26000000 INFO @ Sat, 03 Apr 2021 06:45:25: 29000000 INFO @ Sat, 03 Apr 2021 06:45:27: 18000000 INFO @ Sat, 03 Apr 2021 06:45:30: 27000000 INFO @ Sat, 03 Apr 2021 06:45:31: 30000000 INFO @ Sat, 03 Apr 2021 06:45:34: 19000000 INFO @ Sat, 03 Apr 2021 06:45:35: 28000000 INFO @ Sat, 03 Apr 2021 06:45:37: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:45:37: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:45:37: #1 total tags in treatment: 14697914 INFO @ Sat, 03 Apr 2021 06:45:37: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:45:37: #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 06:45:37: #1 tags after filtering in treatment: 10521725 INFO @ Sat, 03 Apr 2021 06:45:37: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 03 Apr 2021 06:45:37: #1 finished! INFO @ Sat, 03 Apr 2021 06:45:37: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:45:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:45:38: #2 number of paired peaks: 1951 INFO @ Sat, 03 Apr 2021 06:45:38: start model_add_line... INFO @ Sat, 03 Apr 2021 06:45:38: start X-correlation... INFO @ Sat, 03 Apr 2021 06:45:38: end of X-cor INFO @ Sat, 03 Apr 2021 06:45:38: #2 finished! INFO @ Sat, 03 Apr 2021 06:45:38: #2 predicted fragment length is 86 bps INFO @ Sat, 03 Apr 2021 06:45:38: #2 alternative fragment length(s) may be 86 bps INFO @ Sat, 03 Apr 2021 06:45:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.05_model.r WARNING @ Sat, 03 Apr 2021 06:45:38: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:45:38: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Sat, 03 Apr 2021 06:45:38: #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 06:45:38: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:45:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:45:39: 20000000 INFO @ Sat, 03 Apr 2021 06:45:41: 29000000 INFO @ Sat, 03 Apr 2021 06:45:46: 21000000 INFO @ Sat, 03 Apr 2021 06:45:46: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:45:51: 22000000 INFO @ Sat, 03 Apr 2021 06:45:51: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:45:51: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:45:51: #1 total tags in treatment: 14697914 INFO @ Sat, 03 Apr 2021 06:45:51: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:45:51: #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 06:45:51: #1 tags after filtering in treatment: 10521725 INFO @ Sat, 03 Apr 2021 06:45:51: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 03 Apr 2021 06:45:51: #1 finished! INFO @ Sat, 03 Apr 2021 06:45:51: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:45:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:45:52: #2 number of paired peaks: 1951 INFO @ Sat, 03 Apr 2021 06:45:52: start model_add_line... INFO @ Sat, 03 Apr 2021 06:45:52: start X-correlation... INFO @ Sat, 03 Apr 2021 06:45:52: end of X-cor INFO @ Sat, 03 Apr 2021 06:45:52: #2 finished! INFO @ Sat, 03 Apr 2021 06:45:52: #2 predicted fragment length is 86 bps INFO @ Sat, 03 Apr 2021 06:45:52: #2 alternative fragment length(s) may be 86 bps INFO @ Sat, 03 Apr 2021 06:45:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.10_model.r WARNING @ Sat, 03 Apr 2021 06:45:52: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:45:52: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Sat, 03 Apr 2021 06:45:52: #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 06:45:52: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:45:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:45:56: 23000000 INFO @ Sat, 03 Apr 2021 06:46:00: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:46:02: 24000000 INFO @ Sat, 03 Apr 2021 06:46:07: 25000000 INFO @ Sat, 03 Apr 2021 06:46:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:46:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:46:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.05_summits.bed INFO @ Sat, 03 Apr 2021 06:46:12: Done! INFO @ Sat, 03 Apr 2021 06:46:13: 26000000 pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (10306 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:46:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:46:18: 27000000 INFO @ Sat, 03 Apr 2021 06:46:23: 28000000 INFO @ Sat, 03 Apr 2021 06:46:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:46:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:46:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.10_summits.bed INFO @ Sat, 03 Apr 2021 06:46:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5229 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:46:28: 29000000 INFO @ Sat, 03 Apr 2021 06:46:34: 30000000 INFO @ Sat, 03 Apr 2021 06:46:39: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:46:39: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:46:39: #1 total tags in treatment: 14697914 INFO @ Sat, 03 Apr 2021 06:46:39: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:46:39: #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 06:46:39: #1 tags after filtering in treatment: 10521725 INFO @ Sat, 03 Apr 2021 06:46:39: #1 Redundant rate of treatment: 0.28 INFO @ Sat, 03 Apr 2021 06:46:39: #1 finished! INFO @ Sat, 03 Apr 2021 06:46:39: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:46:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:46:40: #2 number of paired peaks: 1951 INFO @ Sat, 03 Apr 2021 06:46:40: start model_add_line... INFO @ Sat, 03 Apr 2021 06:46:40: start X-correlation... INFO @ Sat, 03 Apr 2021 06:46:40: end of X-cor INFO @ Sat, 03 Apr 2021 06:46:40: #2 finished! INFO @ Sat, 03 Apr 2021 06:46:40: #2 predicted fragment length is 86 bps INFO @ Sat, 03 Apr 2021 06:46:40: #2 alternative fragment length(s) may be 86 bps INFO @ Sat, 03 Apr 2021 06:46:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.20_model.r WARNING @ Sat, 03 Apr 2021 06:46:40: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:46:40: #2 You may need to consider one of the other alternative d(s): 86 WARNING @ Sat, 03 Apr 2021 06:46:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:46:40: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:46:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:47:01: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:47:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:47:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:47:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4517990/SRX4517990.20_summits.bed INFO @ Sat, 03 Apr 2021 06:47:13: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1519 records, 4 fields): 4 millis CompletedMACS2peakCalling