Job ID = 14170461 SRX = SRX11760562 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-10T21:49:06 prefetch.2.10.7: 1) Downloading 'SRR15461248'... 2021-12-10T21:49:06 prefetch.2.10.7: Downloading via HTTPS... 2021-12-10T21:51:27 prefetch.2.10.7: HTTPS download succeed 2021-12-10T21:51:27 prefetch.2.10.7: 1) 'SRR15461248' was downloaded successfully 2021-12-10T21:51:27 prefetch.2.10.7: 'SRR15461248' has 0 unresolved dependencies Read 54675539 spots for SRR15461248/SRR15461248.sra Written 54675539 spots for SRR15461248/SRR15461248.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171069 ("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: 00:51:52 54675539 reads; of these: 54675539 (100.00%) were paired; of these: 16544583 (30.26%) aligned concordantly 0 times 18436255 (33.72%) aligned concordantly exactly 1 time 19694701 (36.02%) aligned concordantly >1 times ---- 16544583 pairs aligned concordantly 0 times; of these: 54019 (0.33%) aligned discordantly 1 time ---- 16490564 pairs aligned 0 times concordantly or discordantly; of these: 32981128 mates make up the pairs; of these: 20277609 (61.48%) aligned 0 times 8299862 (25.17%) aligned exactly 1 time 4403657 (13.35%) aligned >1 times 81.46% overall alignment rate Time searching: 00:51:52 Overall time: 00:51:52 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 32 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] 28827504 / 37694727 = 0.7648 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 08:06:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.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 08:06:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:06:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:06:35: 1000000 INFO @ Sat, 11 Dec 2021 08:06:41: 2000000 INFO @ Sat, 11 Dec 2021 08:06:47: 3000000 INFO @ Sat, 11 Dec 2021 08:06:53: 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 @ Sat, 11 Dec 2021 08:06:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.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 08:06:58: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:06:58: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:07:00: 5000000 INFO @ Sat, 11 Dec 2021 08:07:05: 1000000 INFO @ Sat, 11 Dec 2021 08:07:06: 6000000 INFO @ Sat, 11 Dec 2021 08:07:12: 7000000 INFO @ Sat, 11 Dec 2021 08:07:13: 2000000 INFO @ Sat, 11 Dec 2021 08:07:18: 8000000 INFO @ Sat, 11 Dec 2021 08:07:21: 3000000 INFO @ Sat, 11 Dec 2021 08:07:25: 9000000 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 08:07:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.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 08:07:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:07:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:07:28: 4000000 INFO @ Sat, 11 Dec 2021 08:07:31: 10000000 INFO @ Sat, 11 Dec 2021 08:07:37: 1000000 INFO @ Sat, 11 Dec 2021 08:07:37: 5000000 INFO @ Sat, 11 Dec 2021 08:07:37: 11000000 INFO @ Sat, 11 Dec 2021 08:07:44: 12000000 INFO @ Sat, 11 Dec 2021 08:07:45: 2000000 INFO @ Sat, 11 Dec 2021 08:07:45: 6000000 INFO @ Sat, 11 Dec 2021 08:07:50: 13000000 INFO @ Sat, 11 Dec 2021 08:07:53: 3000000 INFO @ Sat, 11 Dec 2021 08:07:53: 7000000 INFO @ Sat, 11 Dec 2021 08:07:57: 14000000 INFO @ Sat, 11 Dec 2021 08:08:01: 4000000 INFO @ Sat, 11 Dec 2021 08:08:01: 8000000 INFO @ Sat, 11 Dec 2021 08:08:03: 15000000 INFO @ Sat, 11 Dec 2021 08:08:09: 5000000 INFO @ Sat, 11 Dec 2021 08:08:09: 9000000 INFO @ Sat, 11 Dec 2021 08:08:09: 16000000 INFO @ Sat, 11 Dec 2021 08:08:16: 17000000 INFO @ Sat, 11 Dec 2021 08:08:17: 6000000 INFO @ Sat, 11 Dec 2021 08:08:17: 10000000 INFO @ Sat, 11 Dec 2021 08:08:22: 18000000 INFO @ Sat, 11 Dec 2021 08:08:25: 7000000 INFO @ Sat, 11 Dec 2021 08:08:25: 11000000 INFO @ Sat, 11 Dec 2021 08:08:29: 19000000 INFO @ Sat, 11 Dec 2021 08:08:33: 8000000 INFO @ Sat, 11 Dec 2021 08:08:34: 12000000 INFO @ Sat, 11 Dec 2021 08:08:35: 20000000 INFO @ Sat, 11 Dec 2021 08:08:41: 21000000 INFO @ Sat, 11 Dec 2021 08:08:42: 9000000 INFO @ Sat, 11 Dec 2021 08:08:42: 13000000 INFO @ Sat, 11 Dec 2021 08:08:47: 22000000 INFO @ Sat, 11 Dec 2021 08:08:50: 10000000 INFO @ Sat, 11 Dec 2021 08:08:51: 14000000 INFO @ Sat, 11 Dec 2021 08:08:53: 23000000 INFO @ Sat, 11 Dec 2021 08:08:59: 24000000 INFO @ Sat, 11 Dec 2021 08:08:59: 11000000 INFO @ Sat, 11 Dec 2021 08:08:59: 15000000 INFO @ Sat, 11 Dec 2021 08:09:05: 25000000 INFO @ Sat, 11 Dec 2021 08:09:07: 12000000 INFO @ Sat, 11 Dec 2021 08:09:07: 16000000 INFO @ Sat, 11 Dec 2021 08:09:12: 26000000 INFO @ Sat, 11 Dec 2021 08:09:16: 17000000 INFO @ Sat, 11 Dec 2021 08:09:16: 13000000 INFO @ Sat, 11 Dec 2021 08:09:19: 27000000 INFO @ Sat, 11 Dec 2021 08:09:23: 18000000 INFO @ Sat, 11 Dec 2021 08:09:25: 14000000 INFO @ Sat, 11 Dec 2021 08:09:26: 28000000 INFO @ Sat, 11 Dec 2021 08:09:31: 19000000 INFO @ Sat, 11 Dec 2021 08:09:32: 29000000 INFO @ Sat, 11 Dec 2021 08:09:33: 15000000 INFO @ Sat, 11 Dec 2021 08:09:38: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:09:39: 30000000 INFO @ Sat, 11 Dec 2021 08:09:40: 16000000 INFO @ Sat, 11 Dec 2021 08:09:46: 21000000 INFO @ Sat, 11 Dec 2021 08:09:46: 31000000 INFO @ Sat, 11 Dec 2021 08:09:48: 17000000 INFO @ Sat, 11 Dec 2021 08:09:49: #1 tag size is determined as 37 bps INFO @ Sat, 11 Dec 2021 08:09:49: #1 tag size = 37 INFO @ Sat, 11 Dec 2021 08:09:49: #1 total tags in treatment: 9315821 INFO @ Sat, 11 Dec 2021 08:09:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:09:49: #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 08:09:49: #1 tags after filtering in treatment: 6508311 INFO @ Sat, 11 Dec 2021 08:09:49: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 11 Dec 2021 08:09:49: #1 finished! INFO @ Sat, 11 Dec 2021 08:09:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:09:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:09:49: #2 number of paired peaks: 1689 INFO @ Sat, 11 Dec 2021 08:09:49: start model_add_line... INFO @ Sat, 11 Dec 2021 08:09:49: start X-correlation... INFO @ Sat, 11 Dec 2021 08:09:49: end of X-cor INFO @ Sat, 11 Dec 2021 08:09:49: #2 finished! INFO @ Sat, 11 Dec 2021 08:09:49: #2 predicted fragment length is 72 bps INFO @ Sat, 11 Dec 2021 08:09:49: #2 alternative fragment length(s) may be 72 bps INFO @ Sat, 11 Dec 2021 08:09:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.05_model.r WARNING @ Sat, 11 Dec 2021 08:09:50: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:09:50: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Sat, 11 Dec 2021 08:09:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:09:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:09:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:09:53: 22000000 INFO @ Sat, 11 Dec 2021 08:09:56: 18000000 INFO @ Sat, 11 Dec 2021 08:10:01: 23000000 INFO @ Sat, 11 Dec 2021 08:10:03: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:10:03: 19000000 INFO @ Sat, 11 Dec 2021 08:10:08: 24000000 INFO @ Sat, 11 Dec 2021 08:10:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:10:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:10:11: 20000000 INFO @ Sat, 11 Dec 2021 08:10:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.05_summits.bed INFO @ Sat, 11 Dec 2021 08:10:11: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11809 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:10:16: 25000000 INFO @ Sat, 11 Dec 2021 08:10:18: 21000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:10:24: 26000000 INFO @ Sat, 11 Dec 2021 08:10:25: 22000000 INFO @ Sat, 11 Dec 2021 08:10:32: 27000000 INFO @ Sat, 11 Dec 2021 08:10:33: 23000000 INFO @ Sat, 11 Dec 2021 08:10:40: 28000000 INFO @ Sat, 11 Dec 2021 08:10:40: 24000000 INFO @ Sat, 11 Dec 2021 08:10:47: 29000000 INFO @ Sat, 11 Dec 2021 08:10:48: 25000000 INFO @ Sat, 11 Dec 2021 08:10:55: 30000000 INFO @ Sat, 11 Dec 2021 08:10:56: 26000000 INFO @ Sat, 11 Dec 2021 08:11:03: 31000000 INFO @ Sat, 11 Dec 2021 08:11:04: 27000000 INFO @ Sat, 11 Dec 2021 08:11:06: #1 tag size is determined as 37 bps INFO @ Sat, 11 Dec 2021 08:11:06: #1 tag size = 37 INFO @ Sat, 11 Dec 2021 08:11:06: #1 total tags in treatment: 9315821 INFO @ Sat, 11 Dec 2021 08:11:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:11:06: #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 08:11:06: #1 tags after filtering in treatment: 6508311 INFO @ Sat, 11 Dec 2021 08:11:06: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 11 Dec 2021 08:11:06: #1 finished! INFO @ Sat, 11 Dec 2021 08:11:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:11:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:11:07: #2 number of paired peaks: 1689 INFO @ Sat, 11 Dec 2021 08:11:07: start model_add_line... INFO @ Sat, 11 Dec 2021 08:11:07: start X-correlation... INFO @ Sat, 11 Dec 2021 08:11:07: end of X-cor INFO @ Sat, 11 Dec 2021 08:11:07: #2 finished! INFO @ Sat, 11 Dec 2021 08:11:07: #2 predicted fragment length is 72 bps INFO @ Sat, 11 Dec 2021 08:11:07: #2 alternative fragment length(s) may be 72 bps INFO @ Sat, 11 Dec 2021 08:11:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.10_model.r WARNING @ Sat, 11 Dec 2021 08:11:07: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:11:07: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Sat, 11 Dec 2021 08:11:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:11:07: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:11:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:11:12: 28000000 INFO @ Sat, 11 Dec 2021 08:11:19: 29000000 INFO @ Sat, 11 Dec 2021 08:11:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:11:26: 30000000 INFO @ Sat, 11 Dec 2021 08:11:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:11:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:11:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.10_summits.bed INFO @ Sat, 11 Dec 2021 08:11:29: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4883 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:11:34: 31000000 INFO @ Sat, 11 Dec 2021 08:11:36: #1 tag size is determined as 37 bps INFO @ Sat, 11 Dec 2021 08:11:36: #1 tag size = 37 INFO @ Sat, 11 Dec 2021 08:11:36: #1 total tags in treatment: 9315821 INFO @ Sat, 11 Dec 2021 08:11:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:11:36: #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 08:11:37: #1 tags after filtering in treatment: 6508311 INFO @ Sat, 11 Dec 2021 08:11:37: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 11 Dec 2021 08:11:37: #1 finished! INFO @ Sat, 11 Dec 2021 08:11:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:11:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:11:37: #2 number of paired peaks: 1689 INFO @ Sat, 11 Dec 2021 08:11:37: start model_add_line... INFO @ Sat, 11 Dec 2021 08:11:37: start X-correlation... INFO @ Sat, 11 Dec 2021 08:11:37: end of X-cor INFO @ Sat, 11 Dec 2021 08:11:37: #2 finished! INFO @ Sat, 11 Dec 2021 08:11:37: #2 predicted fragment length is 72 bps INFO @ Sat, 11 Dec 2021 08:11:37: #2 alternative fragment length(s) may be 72 bps INFO @ Sat, 11 Dec 2021 08:11:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.20_model.r WARNING @ Sat, 11 Dec 2021 08:11:37: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:11:37: #2 You may need to consider one of the other alternative d(s): 72 WARNING @ Sat, 11 Dec 2021 08:11:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:11:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:11:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:11:51: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:11:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:11:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:11:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11760562/SRX11760562.20_summits.bed INFO @ Sat, 11 Dec 2021 08:11:59: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (911 records, 4 fields): 3 millis CompletedMACS2peakCalling