Job ID = 14168882 SRX = SRX9217371 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 41354329 spots for SRR12744934/SRR12744934.sra Written 41354329 spots for SRR12744934/SRR12744934.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170012 ("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: 00:44:24 41354329 reads; of these: 41354329 (100.00%) were paired; of these: 7784874 (18.82%) aligned concordantly 0 times 17280721 (41.79%) aligned concordantly exactly 1 time 16288734 (39.39%) aligned concordantly >1 times ---- 7784874 pairs aligned concordantly 0 times; of these: 968147 (12.44%) aligned discordantly 1 time ---- 6816727 pairs aligned 0 times concordantly or discordantly; of these: 13633454 mates make up the pairs; of these: 12302175 (90.24%) aligned 0 times 457313 (3.35%) aligned exactly 1 time 873966 (6.41%) aligned >1 times 85.13% overall alignment rate Time searching: 00:44:24 Overall time: 00:44:24 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 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] 20689458 / 29358602 = 0.7047 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 @ Fri, 10 Dec 2021 22:33:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.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 @ Fri, 10 Dec 2021 22:33:02: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:33:02: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:33:08: 1000000 INFO @ Fri, 10 Dec 2021 22:33:14: 2000000 INFO @ Fri, 10 Dec 2021 22:33:20: 3000000 INFO @ Fri, 10 Dec 2021 22:33:26: 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 @ Fri, 10 Dec 2021 22:33:31: 5000000 INFO @ Fri, 10 Dec 2021 22:33:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.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 @ Fri, 10 Dec 2021 22:33:32: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:33:32: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:33:38: 6000000 INFO @ Fri, 10 Dec 2021 22:33:38: 1000000 INFO @ Fri, 10 Dec 2021 22:33:44: 2000000 INFO @ Fri, 10 Dec 2021 22:33:44: 7000000 INFO @ Fri, 10 Dec 2021 22:33:49: 3000000 INFO @ Fri, 10 Dec 2021 22:33:50: 8000000 INFO @ Fri, 10 Dec 2021 22:33:54: 4000000 INFO @ Fri, 10 Dec 2021 22:33:57: 9000000 INFO @ Fri, 10 Dec 2021 22:34:00: 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 @ Fri, 10 Dec 2021 22:34:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.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 @ Fri, 10 Dec 2021 22:34:02: #1 read tag files... INFO @ Fri, 10 Dec 2021 22:34:02: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 22:34:03: 10000000 INFO @ Fri, 10 Dec 2021 22:34:05: 6000000 INFO @ Fri, 10 Dec 2021 22:34:08: 1000000 INFO @ Fri, 10 Dec 2021 22:34:09: 11000000 INFO @ Fri, 10 Dec 2021 22:34:11: 7000000 INFO @ Fri, 10 Dec 2021 22:34:13: 2000000 INFO @ Fri, 10 Dec 2021 22:34:16: 12000000 INFO @ Fri, 10 Dec 2021 22:34:16: 8000000 INFO @ Fri, 10 Dec 2021 22:34:19: 3000000 INFO @ Fri, 10 Dec 2021 22:34:22: 9000000 INFO @ Fri, 10 Dec 2021 22:34:22: 13000000 INFO @ Fri, 10 Dec 2021 22:34:25: 4000000 INFO @ Fri, 10 Dec 2021 22:34:27: 10000000 INFO @ Fri, 10 Dec 2021 22:34:28: 14000000 INFO @ Fri, 10 Dec 2021 22:34:30: 5000000 INFO @ Fri, 10 Dec 2021 22:34:33: 11000000 INFO @ Fri, 10 Dec 2021 22:34:35: 15000000 INFO @ Fri, 10 Dec 2021 22:34:36: 6000000 INFO @ Fri, 10 Dec 2021 22:34:38: 12000000 INFO @ Fri, 10 Dec 2021 22:34:41: 16000000 INFO @ Fri, 10 Dec 2021 22:34:41: 7000000 INFO @ Fri, 10 Dec 2021 22:34:44: 13000000 INFO @ Fri, 10 Dec 2021 22:34:47: 8000000 INFO @ Fri, 10 Dec 2021 22:34:47: 17000000 INFO @ Fri, 10 Dec 2021 22:34:49: 14000000 INFO @ Fri, 10 Dec 2021 22:34:52: 9000000 INFO @ Fri, 10 Dec 2021 22:34:54: 18000000 INFO @ Fri, 10 Dec 2021 22:34:55: 15000000 INFO @ Fri, 10 Dec 2021 22:34:58: 10000000 INFO @ Fri, 10 Dec 2021 22:35:00: 19000000 INFO @ Fri, 10 Dec 2021 22:35:00: 16000000 INFO @ Fri, 10 Dec 2021 22:35:03: 11000000 INFO @ Fri, 10 Dec 2021 22:35:06: 17000000 INFO @ Fri, 10 Dec 2021 22:35:06: 20000000 INFO @ Fri, 10 Dec 2021 22:35:08: 12000000 INFO @ Fri, 10 Dec 2021 22:35:11: 18000000 INFO @ Fri, 10 Dec 2021 22:35:12: 21000000 INFO @ Fri, 10 Dec 2021 22:35:14: 13000000 INFO @ Fri, 10 Dec 2021 22:35:17: 19000000 INFO @ Fri, 10 Dec 2021 22:35:19: 22000000 INFO @ Fri, 10 Dec 2021 22:35:19: 14000000 INFO @ Fri, 10 Dec 2021 22:35:22: 20000000 INFO @ Fri, 10 Dec 2021 22:35:25: 15000000 INFO @ Fri, 10 Dec 2021 22:35:25: 23000000 INFO @ Fri, 10 Dec 2021 22:35:27: 21000000 INFO @ Fri, 10 Dec 2021 22:35:30: 16000000 INFO @ Fri, 10 Dec 2021 22:35:31: 24000000 INFO @ Fri, 10 Dec 2021 22:35:33: 22000000 INFO @ Fri, 10 Dec 2021 22:35:36: 17000000 INFO @ Fri, 10 Dec 2021 22:35:38: 25000000 INFO @ Fri, 10 Dec 2021 22:35:38: 23000000 INFO @ Fri, 10 Dec 2021 22:35:41: 18000000 INFO @ Fri, 10 Dec 2021 22:35:44: 24000000 INFO @ Fri, 10 Dec 2021 22:35:44: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 22:35:47: 19000000 INFO @ Fri, 10 Dec 2021 22:35:50: 25000000 INFO @ Fri, 10 Dec 2021 22:35:50: 27000000 INFO @ Fri, 10 Dec 2021 22:35:52: 20000000 INFO @ Fri, 10 Dec 2021 22:35:55: 26000000 INFO @ Fri, 10 Dec 2021 22:35:57: 28000000 INFO @ Fri, 10 Dec 2021 22:35:58: 21000000 INFO @ Fri, 10 Dec 2021 22:36:01: 27000000 INFO @ Fri, 10 Dec 2021 22:36:03: 29000000 INFO @ Fri, 10 Dec 2021 22:36:03: 22000000 INFO @ Fri, 10 Dec 2021 22:36:03: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 22:36:03: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 22:36:03: #1 total tags in treatment: 13322694 INFO @ Fri, 10 Dec 2021 22:36:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:36:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 22:36:03: #1 tags after filtering in treatment: 7352303 INFO @ Fri, 10 Dec 2021 22:36:03: #1 Redundant rate of treatment: 0.45 INFO @ Fri, 10 Dec 2021 22:36:03: #1 finished! INFO @ Fri, 10 Dec 2021 22:36:03: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:36:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:36:04: #2 number of paired peaks: 404 WARNING @ Fri, 10 Dec 2021 22:36:04: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Fri, 10 Dec 2021 22:36:04: start model_add_line... INFO @ Fri, 10 Dec 2021 22:36:04: start X-correlation... INFO @ Fri, 10 Dec 2021 22:36:04: end of X-cor INFO @ Fri, 10 Dec 2021 22:36:04: #2 finished! INFO @ Fri, 10 Dec 2021 22:36:04: #2 predicted fragment length is 102 bps INFO @ Fri, 10 Dec 2021 22:36:04: #2 alternative fragment length(s) may be 102 bps INFO @ Fri, 10 Dec 2021 22:36:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.05_model.r INFO @ Fri, 10 Dec 2021 22:36:04: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:36:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:36:06: 28000000 INFO @ Fri, 10 Dec 2021 22:36:09: 23000000 INFO @ Fri, 10 Dec 2021 22:36:11: 29000000 INFO @ Fri, 10 Dec 2021 22:36:12: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 22:36:12: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 22:36:12: #1 total tags in treatment: 13322694 INFO @ Fri, 10 Dec 2021 22:36:12: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:36:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 22:36:12: #1 tags after filtering in treatment: 7352303 INFO @ Fri, 10 Dec 2021 22:36:12: #1 Redundant rate of treatment: 0.45 INFO @ Fri, 10 Dec 2021 22:36:12: #1 finished! INFO @ Fri, 10 Dec 2021 22:36:12: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:36:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:36:12: #2 number of paired peaks: 404 WARNING @ Fri, 10 Dec 2021 22:36:12: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Fri, 10 Dec 2021 22:36:12: start model_add_line... INFO @ Fri, 10 Dec 2021 22:36:12: start X-correlation... INFO @ Fri, 10 Dec 2021 22:36:12: end of X-cor INFO @ Fri, 10 Dec 2021 22:36:12: #2 finished! INFO @ Fri, 10 Dec 2021 22:36:12: #2 predicted fragment length is 102 bps INFO @ Fri, 10 Dec 2021 22:36:12: #2 alternative fragment length(s) may be 102 bps INFO @ Fri, 10 Dec 2021 22:36:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.10_model.r INFO @ Fri, 10 Dec 2021 22:36:12: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:36:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:36:14: 24000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 22:36:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:36:19: 25000000 INFO @ Fri, 10 Dec 2021 22:36:24: 26000000 INFO @ Fri, 10 Dec 2021 22:36:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.05_peaks.xls INFO @ Fri, 10 Dec 2021 22:36:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:36:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.05_summits.bed INFO @ Fri, 10 Dec 2021 22:36:27: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5031 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 22:36:28: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:36:29: 27000000 INFO @ Fri, 10 Dec 2021 22:36:34: 28000000 INFO @ Fri, 10 Dec 2021 22:36:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.10_peaks.xls INFO @ Fri, 10 Dec 2021 22:36:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:36:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.10_summits.bed INFO @ Fri, 10 Dec 2021 22:36:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1447 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 22:36:39: 29000000 INFO @ Fri, 10 Dec 2021 22:36:39: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 22:36:39: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 22:36:39: #1 total tags in treatment: 13322694 INFO @ Fri, 10 Dec 2021 22:36:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 22:36:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 22:36:39: #1 tags after filtering in treatment: 7352303 INFO @ Fri, 10 Dec 2021 22:36:39: #1 Redundant rate of treatment: 0.45 INFO @ Fri, 10 Dec 2021 22:36:39: #1 finished! INFO @ Fri, 10 Dec 2021 22:36:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 22:36:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 22:36:40: #2 number of paired peaks: 404 WARNING @ Fri, 10 Dec 2021 22:36:40: Fewer paired peaks (404) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 404 pairs to build model! INFO @ Fri, 10 Dec 2021 22:36:40: start model_add_line... INFO @ Fri, 10 Dec 2021 22:36:40: start X-correlation... INFO @ Fri, 10 Dec 2021 22:36:40: end of X-cor INFO @ Fri, 10 Dec 2021 22:36:40: #2 finished! INFO @ Fri, 10 Dec 2021 22:36:40: #2 predicted fragment length is 102 bps INFO @ Fri, 10 Dec 2021 22:36:40: #2 alternative fragment length(s) may be 102 bps INFO @ Fri, 10 Dec 2021 22:36:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.20_model.r INFO @ Fri, 10 Dec 2021 22:36:40: #3 Call peaks... INFO @ Fri, 10 Dec 2021 22:36:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 22:36:55: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 22:37:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.20_peaks.xls INFO @ Fri, 10 Dec 2021 22:37:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 22:37:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9217371/SRX9217371.20_summits.bed INFO @ Fri, 10 Dec 2021 22:37:03: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (597 records, 4 fields): 2 millis CompletedMACS2peakCalling