Job ID = 14170759 SRX = SRX11704571 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-10T23:24:48 prefetch.2.10.7: 1) Downloading 'SRR15402355'... 2021-12-10T23:24:48 prefetch.2.10.7: Downloading via HTTPS... 2021-12-10T23:27:31 prefetch.2.10.7: HTTPS download succeed 2021-12-10T23:27:31 prefetch.2.10.7: 1) 'SRR15402355' was downloaded successfully 2021-12-10T23:27:31 prefetch.2.10.7: 'SRR15402355' has 0 unresolved dependencies Read 81337726 spots for SRR15402355/SRR15402355.sra Written 81337726 spots for SRR15402355/SRR15402355.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171498 ("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: 00:49:55 81337726 reads; of these: 81337726 (100.00%) were paired; of these: 62814505 (77.23%) aligned concordantly 0 times 15591384 (19.17%) aligned concordantly exactly 1 time 2931837 (3.60%) aligned concordantly >1 times ---- 62814505 pairs aligned concordantly 0 times; of these: 2710936 (4.32%) aligned discordantly 1 time ---- 60103569 pairs aligned 0 times concordantly or discordantly; of these: 120207138 mates make up the pairs; of these: 112399590 (93.50%) aligned 0 times 1725987 (1.44%) aligned exactly 1 time 6081561 (5.06%) aligned >1 times 30.91% overall alignment rate Time searching: 00:49:55 Overall time: 00:49:55 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 24 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] 7805801 / 20863904 = 0.3741 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 09:32:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.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 09:32:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:32:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:32:13: 1000000 INFO @ Sat, 11 Dec 2021 09:32:18: 2000000 INFO @ Sat, 11 Dec 2021 09:32:23: 3000000 INFO @ Sat, 11 Dec 2021 09:32:27: 4000000 INFO @ Sat, 11 Dec 2021 09:32:32: 5000000 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 09:32:37: 6000000 INFO @ Sat, 11 Dec 2021 09:32:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.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 09:32:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:32:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:32:42: 7000000 INFO @ Sat, 11 Dec 2021 09:32:43: 1000000 INFO @ Sat, 11 Dec 2021 09:32:47: 8000000 INFO @ Sat, 11 Dec 2021 09:32:48: 2000000 INFO @ Sat, 11 Dec 2021 09:32:52: 9000000 INFO @ Sat, 11 Dec 2021 09:32:52: 3000000 INFO @ Sat, 11 Dec 2021 09:32:57: 10000000 INFO @ Sat, 11 Dec 2021 09:32:57: 4000000 INFO @ Sat, 11 Dec 2021 09:33:02: 11000000 INFO @ Sat, 11 Dec 2021 09:33:02: 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 @ Sat, 11 Dec 2021 09:33:07: 12000000 INFO @ Sat, 11 Dec 2021 09:33:07: 6000000 INFO @ Sat, 11 Dec 2021 09:33:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.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 09:33:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:33:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:33:12: 13000000 INFO @ Sat, 11 Dec 2021 09:33:12: 7000000 INFO @ Sat, 11 Dec 2021 09:33:12: 1000000 INFO @ Sat, 11 Dec 2021 09:33:17: 14000000 INFO @ Sat, 11 Dec 2021 09:33:17: 2000000 INFO @ Sat, 11 Dec 2021 09:33:17: 8000000 INFO @ Sat, 11 Dec 2021 09:33:21: 3000000 INFO @ Sat, 11 Dec 2021 09:33:22: 15000000 INFO @ Sat, 11 Dec 2021 09:33:22: 9000000 INFO @ Sat, 11 Dec 2021 09:33:25: 4000000 INFO @ Sat, 11 Dec 2021 09:33:27: 16000000 INFO @ Sat, 11 Dec 2021 09:33:27: 10000000 INFO @ Sat, 11 Dec 2021 09:33:30: 5000000 INFO @ Sat, 11 Dec 2021 09:33:31: 17000000 INFO @ Sat, 11 Dec 2021 09:33:32: 11000000 INFO @ Sat, 11 Dec 2021 09:33:34: 6000000 INFO @ Sat, 11 Dec 2021 09:33:36: 18000000 INFO @ Sat, 11 Dec 2021 09:33:37: 12000000 INFO @ Sat, 11 Dec 2021 09:33:38: 7000000 INFO @ Sat, 11 Dec 2021 09:33:41: 19000000 INFO @ Sat, 11 Dec 2021 09:33:42: 13000000 INFO @ Sat, 11 Dec 2021 09:33:42: 8000000 INFO @ Sat, 11 Dec 2021 09:33:46: 20000000 INFO @ Sat, 11 Dec 2021 09:33:47: 14000000 INFO @ Sat, 11 Dec 2021 09:33:47: 9000000 INFO @ Sat, 11 Dec 2021 09:33:51: 10000000 INFO @ Sat, 11 Dec 2021 09:33:51: 21000000 INFO @ Sat, 11 Dec 2021 09:33:51: 15000000 INFO @ Sat, 11 Dec 2021 09:33:55: 11000000 INFO @ Sat, 11 Dec 2021 09:33:56: 22000000 INFO @ Sat, 11 Dec 2021 09:33:56: 16000000 INFO @ Sat, 11 Dec 2021 09:33:59: 12000000 INFO @ Sat, 11 Dec 2021 09:34:00: 23000000 INFO @ Sat, 11 Dec 2021 09:34:01: 17000000 INFO @ Sat, 11 Dec 2021 09:34:04: 13000000 INFO @ Sat, 11 Dec 2021 09:34:05: 24000000 INFO @ Sat, 11 Dec 2021 09:34:06: 18000000 INFO @ Sat, 11 Dec 2021 09:34:08: 14000000 INFO @ Sat, 11 Dec 2021 09:34:10: 25000000 INFO @ Sat, 11 Dec 2021 09:34:11: 19000000 INFO @ Sat, 11 Dec 2021 09:34:12: 15000000 INFO @ Sat, 11 Dec 2021 09:34:15: 26000000 INFO @ Sat, 11 Dec 2021 09:34:16: 20000000 INFO @ Sat, 11 Dec 2021 09:34:17: 16000000 INFO @ Sat, 11 Dec 2021 09:34:19: 27000000 INFO @ Sat, 11 Dec 2021 09:34:21: 17000000 INFO @ Sat, 11 Dec 2021 09:34:21: 21000000 INFO @ Sat, 11 Dec 2021 09:34:24: 28000000 INFO @ Sat, 11 Dec 2021 09:34:25: 18000000 INFO @ Sat, 11 Dec 2021 09:34:25: 22000000 INFO @ Sat, 11 Dec 2021 09:34:28: 29000000 INFO @ Sat, 11 Dec 2021 09:34:29: 19000000 INFO @ Sat, 11 Dec 2021 09:34:30: 23000000 INFO @ Sat, 11 Dec 2021 09:34:32: 30000000 INFO @ Sat, 11 Dec 2021 09:34:34: 20000000 INFO @ Sat, 11 Dec 2021 09:34:35: 24000000 INFO @ Sat, 11 Dec 2021 09:34:37: 31000000 INFO @ Sat, 11 Dec 2021 09:34:38: 21000000 INFO @ Sat, 11 Dec 2021 09:34:40: 25000000 INFO @ Sat, 11 Dec 2021 09:34:42: 22000000 INFO @ Sat, 11 Dec 2021 09:34:42: 32000000 INFO @ Sat, 11 Dec 2021 09:34:45: 26000000 INFO @ Sat, 11 Dec 2021 09:34:45: 23000000 INFO @ Sat, 11 Dec 2021 09:34:47: 33000000 INFO @ Sat, 11 Dec 2021 09:34:49: 27000000 INFO @ Sat, 11 Dec 2021 09:34:50: 24000000 INFO @ Sat, 11 Dec 2021 09:34:51: 34000000 INFO @ Sat, 11 Dec 2021 09:34:53: 28000000 INFO @ Sat, 11 Dec 2021 09:34:54: 25000000 INFO @ Sat, 11 Dec 2021 09:34:55: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:34:55: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:34:55: #1 total tags in treatment: 11997637 INFO @ Sat, 11 Dec 2021 09:34:55: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:34:55: #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 09:34:55: #1 tags after filtering in treatment: 8075616 INFO @ Sat, 11 Dec 2021 09:34:55: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 11 Dec 2021 09:34:55: #1 finished! INFO @ Sat, 11 Dec 2021 09:34:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:34:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:34:56: #2 number of paired peaks: 2755 INFO @ Sat, 11 Dec 2021 09:34:56: start model_add_line... INFO @ Sat, 11 Dec 2021 09:34:56: start X-correlation... INFO @ Sat, 11 Dec 2021 09:34:56: end of X-cor INFO @ Sat, 11 Dec 2021 09:34:56: #2 finished! INFO @ Sat, 11 Dec 2021 09:34:56: #2 predicted fragment length is 76 bps INFO @ Sat, 11 Dec 2021 09:34:56: #2 alternative fragment length(s) may be 76 bps INFO @ Sat, 11 Dec 2021 09:34:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.05_model.r WARNING @ Sat, 11 Dec 2021 09:34:56: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:34:56: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sat, 11 Dec 2021 09:34:56: #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 09:34:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:34:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:34:57: 29000000 INFO @ Sat, 11 Dec 2021 09:34:58: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:35:02: 27000000 INFO @ Sat, 11 Dec 2021 09:35:02: 30000000 INFO @ Sat, 11 Dec 2021 09:35:05: 28000000 INFO @ Sat, 11 Dec 2021 09:35:06: 31000000 INFO @ Sat, 11 Dec 2021 09:35:08: 29000000 INFO @ Sat, 11 Dec 2021 09:35:11: 32000000 INFO @ Sat, 11 Dec 2021 09:35:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:35:12: 30000000 INFO @ Sat, 11 Dec 2021 09:35:16: 33000000 INFO @ Sat, 11 Dec 2021 09:35:16: 31000000 INFO @ Sat, 11 Dec 2021 09:35:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:35:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:35:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.05_summits.bed INFO @ Sat, 11 Dec 2021 09:35:20: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (12677 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:35:20: 32000000 INFO @ Sat, 11 Dec 2021 09:35:20: 34000000 INFO @ Sat, 11 Dec 2021 09:35:24: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:35:24: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:35:24: #1 total tags in treatment: 11997637 INFO @ Sat, 11 Dec 2021 09:35:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:35:24: #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 09:35:24: #1 tags after filtering in treatment: 8075616 INFO @ Sat, 11 Dec 2021 09:35:24: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 11 Dec 2021 09:35:24: #1 finished! INFO @ Sat, 11 Dec 2021 09:35:24: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:35:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:35:24: 33000000 INFO @ Sat, 11 Dec 2021 09:35:25: #2 number of paired peaks: 2755 INFO @ Sat, 11 Dec 2021 09:35:25: start model_add_line... INFO @ Sat, 11 Dec 2021 09:35:25: start X-correlation... INFO @ Sat, 11 Dec 2021 09:35:25: end of X-cor INFO @ Sat, 11 Dec 2021 09:35:25: #2 finished! INFO @ Sat, 11 Dec 2021 09:35:25: #2 predicted fragment length is 76 bps INFO @ Sat, 11 Dec 2021 09:35:25: #2 alternative fragment length(s) may be 76 bps INFO @ Sat, 11 Dec 2021 09:35:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.10_model.r WARNING @ Sat, 11 Dec 2021 09:35:25: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:35:25: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sat, 11 Dec 2021 09:35:25: #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 09:35:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:35:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:35:28: 34000000 INFO @ Sat, 11 Dec 2021 09:35:31: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:35:31: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:35:31: #1 total tags in treatment: 11997637 INFO @ Sat, 11 Dec 2021 09:35:31: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:35:31: #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 09:35:31: #1 tags after filtering in treatment: 8075616 INFO @ Sat, 11 Dec 2021 09:35:31: #1 Redundant rate of treatment: 0.33 INFO @ Sat, 11 Dec 2021 09:35:31: #1 finished! INFO @ Sat, 11 Dec 2021 09:35:31: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:35:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:35:32: #2 number of paired peaks: 2755 INFO @ Sat, 11 Dec 2021 09:35:32: start model_add_line... INFO @ Sat, 11 Dec 2021 09:35:32: start X-correlation... INFO @ Sat, 11 Dec 2021 09:35:32: end of X-cor INFO @ Sat, 11 Dec 2021 09:35:32: #2 finished! INFO @ Sat, 11 Dec 2021 09:35:32: #2 predicted fragment length is 76 bps INFO @ Sat, 11 Dec 2021 09:35:32: #2 alternative fragment length(s) may be 76 bps INFO @ Sat, 11 Dec 2021 09:35:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.20_model.r WARNING @ Sat, 11 Dec 2021 09:35:32: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:35:32: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sat, 11 Dec 2021 09:35:32: #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 09:35:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:35:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:35:40: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:35:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:35:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:35:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.10_summits.bed INFO @ Sat, 11 Dec 2021 09:35:48: Done! INFO @ Sat, 11 Dec 2021 09:35:48: #3 Call peaks for each chromosome... pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (7954 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:35:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:35:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:35:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11704571/SRX11704571.20_summits.bed INFO @ Sat, 11 Dec 2021 09:35:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3932 records, 4 fields): 5 millis CompletedMACS2peakCalling