Job ID = 14170752 SRX = SRX11704569 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-10T23:23:03 prefetch.2.10.7: 1) Downloading 'SRR15402353'... 2021-12-10T23:23:03 prefetch.2.10.7: Downloading via HTTPS... 2021-12-10T23:26:30 prefetch.2.10.7: HTTPS download succeed 2021-12-10T23:26:30 prefetch.2.10.7: 1) 'SRR15402353' was downloaded successfully 2021-12-10T23:26:30 prefetch.2.10.7: 'SRR15402353' has 0 unresolved dependencies Read 114810012 spots for SRR15402353/SRR15402353.sra Written 114810012 spots for SRR15402353/SRR15402353.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171553 ("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: 01:03:29 114810012 reads; of these: 114810012 (100.00%) were paired; of these: 106709299 (92.94%) aligned concordantly 0 times 7321259 (6.38%) aligned concordantly exactly 1 time 779454 (0.68%) aligned concordantly >1 times ---- 106709299 pairs aligned concordantly 0 times; of these: 1847445 (1.73%) aligned discordantly 1 time ---- 104861854 pairs aligned 0 times concordantly or discordantly; of these: 209723708 mates make up the pairs; of these: 196042921 (93.48%) aligned 0 times 546343 (0.26%) aligned exactly 1 time 13134444 (6.26%) aligned >1 times 14.62% overall alignment rate Time searching: 01:03:29 Overall time: 01:03:29 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] 2059305 / 9751773 = 0.2112 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 09:45:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.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 09:45:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:45:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:45:50: 1000000 INFO @ Sat, 11 Dec 2021 09:45:55: 2000000 INFO @ Sat, 11 Dec 2021 09:46:01: 3000000 INFO @ Sat, 11 Dec 2021 09:46:06: 4000000 INFO @ Sat, 11 Dec 2021 09:46:12: 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 09:46:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.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 09:46:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:46:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:46:17: 6000000 INFO @ Sat, 11 Dec 2021 09:46:20: 1000000 INFO @ Sat, 11 Dec 2021 09:46:23: 7000000 INFO @ Sat, 11 Dec 2021 09:46:25: 2000000 INFO @ Sat, 11 Dec 2021 09:46:29: 8000000 INFO @ Sat, 11 Dec 2021 09:46:31: 3000000 INFO @ Sat, 11 Dec 2021 09:46:34: 9000000 INFO @ Sat, 11 Dec 2021 09:46:36: 4000000 INFO @ Sat, 11 Dec 2021 09:46:39: 10000000 INFO @ Sat, 11 Dec 2021 09:46:41: 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 09:46:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.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 09:46:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:46:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:46:45: 11000000 INFO @ Sat, 11 Dec 2021 09:46:47: 6000000 INFO @ Sat, 11 Dec 2021 09:46:51: 1000000 INFO @ Sat, 11 Dec 2021 09:46:51: 12000000 INFO @ Sat, 11 Dec 2021 09:46:53: 7000000 INFO @ Sat, 11 Dec 2021 09:46:57: 2000000 INFO @ Sat, 11 Dec 2021 09:46:57: 13000000 INFO @ Sat, 11 Dec 2021 09:46:59: 8000000 INFO @ Sat, 11 Dec 2021 09:47:02: 14000000 INFO @ Sat, 11 Dec 2021 09:47:03: 3000000 INFO @ Sat, 11 Dec 2021 09:47:04: 9000000 INFO @ Sat, 11 Dec 2021 09:47:07: 15000000 INFO @ Sat, 11 Dec 2021 09:47:08: 4000000 INFO @ Sat, 11 Dec 2021 09:47:10: 10000000 INFO @ Sat, 11 Dec 2021 09:47:12: 16000000 INFO @ Sat, 11 Dec 2021 09:47:14: 5000000 INFO @ Sat, 11 Dec 2021 09:47:16: 11000000 INFO @ Sat, 11 Dec 2021 09:47:17: 17000000 INFO @ Sat, 11 Dec 2021 09:47:20: 6000000 INFO @ Sat, 11 Dec 2021 09:47:21: 12000000 INFO @ Sat, 11 Dec 2021 09:47:23: 18000000 INFO @ Sat, 11 Dec 2021 09:47:26: 7000000 INFO @ Sat, 11 Dec 2021 09:47:27: 13000000 INFO @ Sat, 11 Dec 2021 09:47:28: 19000000 INFO @ Sat, 11 Dec 2021 09:47:31: 8000000 INFO @ Sat, 11 Dec 2021 09:47:32: 14000000 INFO @ Sat, 11 Dec 2021 09:47:33: 20000000 INFO @ Sat, 11 Dec 2021 09:47:37: 15000000 INFO @ Sat, 11 Dec 2021 09:47:37: 9000000 INFO @ Sat, 11 Dec 2021 09:47:38: 21000000 INFO @ Sat, 11 Dec 2021 09:47:42: 16000000 INFO @ Sat, 11 Dec 2021 09:47:43: 22000000 INFO @ Sat, 11 Dec 2021 09:47:43: 10000000 INFO @ Sat, 11 Dec 2021 09:47:47: 17000000 INFO @ Sat, 11 Dec 2021 09:47:47: 23000000 INFO @ Sat, 11 Dec 2021 09:47:49: 11000000 INFO @ Sat, 11 Dec 2021 09:47:52: 24000000 INFO @ Sat, 11 Dec 2021 09:47:52: 18000000 INFO @ Sat, 11 Dec 2021 09:47:54: 12000000 INFO @ Sat, 11 Dec 2021 09:47:57: 25000000 INFO @ Sat, 11 Dec 2021 09:47:57: 19000000 INFO @ Sat, 11 Dec 2021 09:48:00: 13000000 INFO @ Sat, 11 Dec 2021 09:48:02: 26000000 INFO @ Sat, 11 Dec 2021 09:48:03: 20000000 INFO @ Sat, 11 Dec 2021 09:48:05: 14000000 INFO @ Sat, 11 Dec 2021 09:48:07: 27000000 INFO @ Sat, 11 Dec 2021 09:48:08: 21000000 INFO @ Sat, 11 Dec 2021 09:48:10: 15000000 INFO @ Sat, 11 Dec 2021 09:48:12: 22000000 INFO @ Sat, 11 Dec 2021 09:48:13: 28000000 INFO @ Sat, 11 Dec 2021 09:48:15: 16000000 INFO @ Sat, 11 Dec 2021 09:48:17: 23000000 INFO @ Sat, 11 Dec 2021 09:48:19: 29000000 INFO @ Sat, 11 Dec 2021 09:48:20: 17000000 INFO @ Sat, 11 Dec 2021 09:48:21: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:48:21: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:48:21: #1 total tags in treatment: 6571039 INFO @ Sat, 11 Dec 2021 09:48:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:48:21: #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 09:48:21: #1 tags after filtering in treatment: 4317980 INFO @ Sat, 11 Dec 2021 09:48:21: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 11 Dec 2021 09:48:21: #1 finished! INFO @ Sat, 11 Dec 2021 09:48:21: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:48:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:48:22: #2 number of paired peaks: 7915 INFO @ Sat, 11 Dec 2021 09:48:22: start model_add_line... INFO @ Sat, 11 Dec 2021 09:48:22: start X-correlation... INFO @ Sat, 11 Dec 2021 09:48:22: end of X-cor INFO @ Sat, 11 Dec 2021 09:48:22: #2 finished! INFO @ Sat, 11 Dec 2021 09:48:22: #2 predicted fragment length is 76 bps INFO @ Sat, 11 Dec 2021 09:48:22: #2 alternative fragment length(s) may be 76 bps INFO @ Sat, 11 Dec 2021 09:48:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.05_model.r WARNING @ Sat, 11 Dec 2021 09:48:22: #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 09:48:22: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sat, 11 Dec 2021 09:48:22: #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 09:48:22: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:48:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:48:22: 24000000 INFO @ Sat, 11 Dec 2021 09:48:25: 18000000 INFO @ Sat, 11 Dec 2021 09:48:27: 25000000 INFO @ Sat, 11 Dec 2021 09:48:30: 19000000 INFO @ Sat, 11 Dec 2021 09:48:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:48:32: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:48:35: 20000000 INFO @ Sat, 11 Dec 2021 09:48:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:48:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:48:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.05_summits.bed INFO @ Sat, 11 Dec 2021 09:48:36: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (17507 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:48:37: 27000000 INFO @ Sat, 11 Dec 2021 09:48:40: 21000000 INFO @ Sat, 11 Dec 2021 09:48:43: 28000000 INFO @ Sat, 11 Dec 2021 09:48:45: 22000000 INFO @ Sat, 11 Dec 2021 09:48:48: 29000000 INFO @ Sat, 11 Dec 2021 09:48:50: 23000000 INFO @ Sat, 11 Dec 2021 09:48:51: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:48:51: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:48:51: #1 total tags in treatment: 6571039 INFO @ Sat, 11 Dec 2021 09:48:51: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:48:51: #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 09:48:51: #1 tags after filtering in treatment: 4317980 INFO @ Sat, 11 Dec 2021 09:48:51: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 11 Dec 2021 09:48:51: #1 finished! INFO @ Sat, 11 Dec 2021 09:48:51: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:48:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:48:52: #2 number of paired peaks: 7915 INFO @ Sat, 11 Dec 2021 09:48:52: start model_add_line... INFO @ Sat, 11 Dec 2021 09:48:52: start X-correlation... INFO @ Sat, 11 Dec 2021 09:48:52: end of X-cor INFO @ Sat, 11 Dec 2021 09:48:52: #2 finished! INFO @ Sat, 11 Dec 2021 09:48:52: #2 predicted fragment length is 76 bps INFO @ Sat, 11 Dec 2021 09:48:52: #2 alternative fragment length(s) may be 76 bps INFO @ Sat, 11 Dec 2021 09:48:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.10_model.r WARNING @ Sat, 11 Dec 2021 09:48:52: #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 09:48:52: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sat, 11 Dec 2021 09:48:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:48:52: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:48:52: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:48:54: 24000000 INFO @ Sat, 11 Dec 2021 09:48:59: 25000000 INFO @ Sat, 11 Dec 2021 09:49:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:49:03: 26000000 INFO @ Sat, 11 Dec 2021 09:49:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:49:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:49:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.10_summits.bed INFO @ Sat, 11 Dec 2021 09:49:06: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11235 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:49:08: 27000000 INFO @ Sat, 11 Dec 2021 09:49:13: 28000000 INFO @ Sat, 11 Dec 2021 09:49:19: 29000000 INFO @ Sat, 11 Dec 2021 09:49:21: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 09:49:21: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 09:49:21: #1 total tags in treatment: 6571039 INFO @ Sat, 11 Dec 2021 09:49:21: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:49:21: #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 09:49:21: #1 tags after filtering in treatment: 4317980 INFO @ Sat, 11 Dec 2021 09:49:21: #1 Redundant rate of treatment: 0.34 INFO @ Sat, 11 Dec 2021 09:49:21: #1 finished! INFO @ Sat, 11 Dec 2021 09:49:21: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:49:21: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:49:22: #2 number of paired peaks: 7915 INFO @ Sat, 11 Dec 2021 09:49:22: start model_add_line... INFO @ Sat, 11 Dec 2021 09:49:22: start X-correlation... INFO @ Sat, 11 Dec 2021 09:49:22: end of X-cor INFO @ Sat, 11 Dec 2021 09:49:22: #2 finished! INFO @ Sat, 11 Dec 2021 09:49:22: #2 predicted fragment length is 76 bps INFO @ Sat, 11 Dec 2021 09:49:22: #2 alternative fragment length(s) may be 76 bps INFO @ Sat, 11 Dec 2021 09:49:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.20_model.r WARNING @ Sat, 11 Dec 2021 09:49:22: #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 09:49:22: #2 You may need to consider one of the other alternative d(s): 76 WARNING @ Sat, 11 Dec 2021 09:49:22: #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 09:49:22: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:49:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:49:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:49:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:49:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:49:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX11704569/SRX11704569.20_summits.bed INFO @ Sat, 11 Dec 2021 09:49:36: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5626 records, 4 fields): 7 millis CompletedMACS2peakCalling