Job ID = 14167262 SRX = SRX8076965 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17299209 spots for SRR11504837/SRR11504837.sra Written 17299209 spots for SRR11504837/SRR11504837.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167899 ("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: 00:11:34 17299209 reads; of these: 17299209 (100.00%) were paired; of these: 8413109 (48.63%) aligned concordantly 0 times 7947675 (45.94%) aligned concordantly exactly 1 time 938425 (5.42%) aligned concordantly >1 times ---- 8413109 pairs aligned concordantly 0 times; of these: 1197640 (14.24%) aligned discordantly 1 time ---- 7215469 pairs aligned 0 times concordantly or discordantly; of these: 14430938 mates make up the pairs; of these: 13444511 (93.16%) aligned 0 times 708253 (4.91%) aligned exactly 1 time 278174 (1.93%) aligned >1 times 61.14% overall alignment rate Time searching: 00:11:34 Overall time: 00:11:34 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 12 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] 1781543 / 10080468 = 0.1767 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 11:40:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.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 11:40:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:40:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:40:29: 1000000 INFO @ Fri, 10 Dec 2021 11:40:35: 2000000 INFO @ Fri, 10 Dec 2021 11:40:41: 3000000 INFO @ Fri, 10 Dec 2021 11:40:47: 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 11:40:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.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 11:40:53: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:40:53: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:40:54: 5000000 INFO @ Fri, 10 Dec 2021 11:40:59: 1000000 INFO @ Fri, 10 Dec 2021 11:41:01: 6000000 INFO @ Fri, 10 Dec 2021 11:41:06: 2000000 INFO @ Fri, 10 Dec 2021 11:41:08: 7000000 INFO @ Fri, 10 Dec 2021 11:41:13: 3000000 INFO @ Fri, 10 Dec 2021 11:41:14: 8000000 INFO @ Fri, 10 Dec 2021 11:41:20: 4000000 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 11:41:21: 9000000 INFO @ Fri, 10 Dec 2021 11:41:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.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 11:41:23: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:41:23: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:41:28: 5000000 INFO @ Fri, 10 Dec 2021 11:41:28: 10000000 INFO @ Fri, 10 Dec 2021 11:41:29: 1000000 INFO @ Fri, 10 Dec 2021 11:41:35: 6000000 INFO @ Fri, 10 Dec 2021 11:41:35: 2000000 INFO @ Fri, 10 Dec 2021 11:41:35: 11000000 INFO @ Fri, 10 Dec 2021 11:41:41: 3000000 INFO @ Fri, 10 Dec 2021 11:41:42: 7000000 INFO @ Fri, 10 Dec 2021 11:41:42: 12000000 INFO @ Fri, 10 Dec 2021 11:41:47: 4000000 INFO @ Fri, 10 Dec 2021 11:41:49: 8000000 INFO @ Fri, 10 Dec 2021 11:41:49: 13000000 INFO @ Fri, 10 Dec 2021 11:41:53: 5000000 INFO @ Fri, 10 Dec 2021 11:41:56: 9000000 INFO @ Fri, 10 Dec 2021 11:41:56: 14000000 INFO @ Fri, 10 Dec 2021 11:41:59: 6000000 INFO @ Fri, 10 Dec 2021 11:42:03: 10000000 INFO @ Fri, 10 Dec 2021 11:42:03: 15000000 INFO @ Fri, 10 Dec 2021 11:42:06: 7000000 INFO @ Fri, 10 Dec 2021 11:42:10: 11000000 INFO @ Fri, 10 Dec 2021 11:42:10: 16000000 INFO @ Fri, 10 Dec 2021 11:42:12: 8000000 INFO @ Fri, 10 Dec 2021 11:42:17: 17000000 INFO @ Fri, 10 Dec 2021 11:42:17: 12000000 INFO @ Fri, 10 Dec 2021 11:42:18: 9000000 INFO @ Fri, 10 Dec 2021 11:42:21: #1 tag size is determined as 43 bps INFO @ Fri, 10 Dec 2021 11:42:21: #1 tag size = 43 INFO @ Fri, 10 Dec 2021 11:42:21: #1 total tags in treatment: 7256156 INFO @ Fri, 10 Dec 2021 11:42:21: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:42:21: #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 11:42:21: #1 tags after filtering in treatment: 6837507 INFO @ Fri, 10 Dec 2021 11:42:21: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 11:42:21: #1 finished! INFO @ Fri, 10 Dec 2021 11:42:21: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:42:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:42:22: #2 number of paired peaks: 6950 INFO @ Fri, 10 Dec 2021 11:42:22: start model_add_line... INFO @ Fri, 10 Dec 2021 11:42:22: start X-correlation... INFO @ Fri, 10 Dec 2021 11:42:22: end of X-cor INFO @ Fri, 10 Dec 2021 11:42:22: #2 finished! INFO @ Fri, 10 Dec 2021 11:42:22: #2 predicted fragment length is 258 bps INFO @ Fri, 10 Dec 2021 11:42:22: #2 alternative fragment length(s) may be 4,258 bps INFO @ Fri, 10 Dec 2021 11:42:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.05_model.r INFO @ Fri, 10 Dec 2021 11:42:22: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:42:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:42:24: 10000000 INFO @ Fri, 10 Dec 2021 11:42:24: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:42:30: 11000000 INFO @ Fri, 10 Dec 2021 11:42:31: 14000000 INFO @ Fri, 10 Dec 2021 11:42:36: 12000000 INFO @ Fri, 10 Dec 2021 11:42:38: 15000000 INFO @ Fri, 10 Dec 2021 11:42:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:42:42: 13000000 INFO @ Fri, 10 Dec 2021 11:42:45: 16000000 INFO @ Fri, 10 Dec 2021 11:42:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:42:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:42:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.05_summits.bed INFO @ Fri, 10 Dec 2021 11:42:48: 14000000 INFO @ Fri, 10 Dec 2021 11:42:48: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (867 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:42:52: 17000000 INFO @ Fri, 10 Dec 2021 11:42:54: 15000000 INFO @ Fri, 10 Dec 2021 11:42:56: #1 tag size is determined as 43 bps INFO @ Fri, 10 Dec 2021 11:42:56: #1 tag size = 43 INFO @ Fri, 10 Dec 2021 11:42:56: #1 total tags in treatment: 7256156 INFO @ Fri, 10 Dec 2021 11:42:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:42:56: #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 11:42:56: #1 tags after filtering in treatment: 6837507 INFO @ Fri, 10 Dec 2021 11:42:56: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 11:42:56: #1 finished! INFO @ Fri, 10 Dec 2021 11:42:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:42:56: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:42:57: #2 number of paired peaks: 6950 INFO @ Fri, 10 Dec 2021 11:42:57: start model_add_line... INFO @ Fri, 10 Dec 2021 11:42:57: start X-correlation... INFO @ Fri, 10 Dec 2021 11:42:57: end of X-cor INFO @ Fri, 10 Dec 2021 11:42:57: #2 finished! INFO @ Fri, 10 Dec 2021 11:42:57: #2 predicted fragment length is 258 bps INFO @ Fri, 10 Dec 2021 11:42:57: #2 alternative fragment length(s) may be 4,258 bps INFO @ Fri, 10 Dec 2021 11:42:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.10_model.r INFO @ Fri, 10 Dec 2021 11:42:57: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:42:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:43:00: 16000000 INFO @ Fri, 10 Dec 2021 11:43:06: 17000000 INFO @ Fri, 10 Dec 2021 11:43:09: #1 tag size is determined as 43 bps INFO @ Fri, 10 Dec 2021 11:43:09: #1 tag size = 43 INFO @ Fri, 10 Dec 2021 11:43:09: #1 total tags in treatment: 7256156 INFO @ Fri, 10 Dec 2021 11:43:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:43:09: #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 11:43:09: #1 tags after filtering in treatment: 6837507 INFO @ Fri, 10 Dec 2021 11:43:09: #1 Redundant rate of treatment: 0.06 INFO @ Fri, 10 Dec 2021 11:43:09: #1 finished! INFO @ Fri, 10 Dec 2021 11:43:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:43:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:43:10: #2 number of paired peaks: 6950 INFO @ Fri, 10 Dec 2021 11:43:10: start model_add_line... INFO @ Fri, 10 Dec 2021 11:43:10: start X-correlation... INFO @ Fri, 10 Dec 2021 11:43:10: end of X-cor INFO @ Fri, 10 Dec 2021 11:43:10: #2 finished! INFO @ Fri, 10 Dec 2021 11:43:10: #2 predicted fragment length is 258 bps INFO @ Fri, 10 Dec 2021 11:43:10: #2 alternative fragment length(s) may be 4,258 bps INFO @ Fri, 10 Dec 2021 11:43:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.20_model.r INFO @ Fri, 10 Dec 2021 11:43:10: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:43:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:43:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:43:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:43:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:43:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.10_summits.bed INFO @ Fri, 10 Dec 2021 11:43:23: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (353 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:43:28: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:43:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:43:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:43:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8076965/SRX8076965.20_summits.bed INFO @ Fri, 10 Dec 2021 11:43:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (95 records, 4 fields): 1 millis CompletedMACS2peakCalling