Job ID = 14172419 SRX = SRX7628882 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 16869306 spots for SRR10963244/SRR10963244.sra Written 16869306 spots for SRR10963244/SRR10963244.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172923 ("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: 00:18:28 16869306 reads; of these: 16869306 (100.00%) were paired; of these: 6539598 (38.77%) aligned concordantly 0 times 7660523 (45.41%) aligned concordantly exactly 1 time 2669185 (15.82%) aligned concordantly >1 times ---- 6539598 pairs aligned concordantly 0 times; of these: 46187 (0.71%) aligned discordantly 1 time ---- 6493411 pairs aligned 0 times concordantly or discordantly; of these: 12986822 mates make up the pairs; of these: 12423745 (95.66%) aligned 0 times 285644 (2.20%) aligned exactly 1 time 277433 (2.14%) aligned >1 times 63.18% overall alignment rate Time searching: 00:18:28 Overall time: 00:18:28 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 8 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] 628916 / 10371878 = 0.0606 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 15:45:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.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 15:45:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:45:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:45:33: 1000000 INFO @ Sat, 11 Dec 2021 15:45:40: 2000000 INFO @ Sat, 11 Dec 2021 15:45:47: 3000000 INFO @ Sat, 11 Dec 2021 15:45:54: 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 15:45:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.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 15:45:57: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:45:57: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:46:01: 5000000 INFO @ Sat, 11 Dec 2021 15:46:03: 1000000 INFO @ Sat, 11 Dec 2021 15:46:09: 6000000 INFO @ Sat, 11 Dec 2021 15:46:10: 2000000 INFO @ Sat, 11 Dec 2021 15:46:16: 7000000 INFO @ Sat, 11 Dec 2021 15:46:17: 3000000 INFO @ Sat, 11 Dec 2021 15:46:23: 4000000 INFO @ Sat, 11 Dec 2021 15:46:24: 8000000 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 15:46:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.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 15:46:27: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:46:27: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:46:30: 5000000 INFO @ Sat, 11 Dec 2021 15:46:32: 9000000 INFO @ Sat, 11 Dec 2021 15:46:33: 1000000 INFO @ Sat, 11 Dec 2021 15:46:36: 6000000 INFO @ Sat, 11 Dec 2021 15:46:39: 10000000 INFO @ Sat, 11 Dec 2021 15:46:40: 2000000 INFO @ Sat, 11 Dec 2021 15:46:43: 7000000 INFO @ Sat, 11 Dec 2021 15:46:47: 3000000 INFO @ Sat, 11 Dec 2021 15:46:47: 11000000 INFO @ Sat, 11 Dec 2021 15:46:49: 8000000 INFO @ Sat, 11 Dec 2021 15:46:53: 4000000 INFO @ Sat, 11 Dec 2021 15:46:55: 12000000 INFO @ Sat, 11 Dec 2021 15:46:56: 9000000 INFO @ Sat, 11 Dec 2021 15:47:00: 5000000 INFO @ Sat, 11 Dec 2021 15:47:02: 13000000 INFO @ Sat, 11 Dec 2021 15:47:03: 10000000 INFO @ Sat, 11 Dec 2021 15:47:06: 6000000 INFO @ Sat, 11 Dec 2021 15:47:09: 11000000 INFO @ Sat, 11 Dec 2021 15:47:10: 14000000 INFO @ Sat, 11 Dec 2021 15:47:13: 7000000 INFO @ Sat, 11 Dec 2021 15:47:16: 12000000 INFO @ Sat, 11 Dec 2021 15:47:18: 15000000 INFO @ Sat, 11 Dec 2021 15:47:19: 8000000 INFO @ Sat, 11 Dec 2021 15:47:22: 13000000 INFO @ Sat, 11 Dec 2021 15:47:26: 16000000 INFO @ Sat, 11 Dec 2021 15:47:26: 9000000 INFO @ Sat, 11 Dec 2021 15:47:29: 14000000 INFO @ Sat, 11 Dec 2021 15:47:33: 10000000 INFO @ Sat, 11 Dec 2021 15:47:33: 17000000 INFO @ Sat, 11 Dec 2021 15:47:35: 15000000 INFO @ Sat, 11 Dec 2021 15:47:39: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:47:41: 18000000 INFO @ Sat, 11 Dec 2021 15:47:42: 16000000 INFO @ Sat, 11 Dec 2021 15:47:46: 12000000 INFO @ Sat, 11 Dec 2021 15:47:49: 19000000 INFO @ Sat, 11 Dec 2021 15:47:49: 17000000 INFO @ Sat, 11 Dec 2021 15:47:52: 13000000 INFO @ Sat, 11 Dec 2021 15:47:55: 18000000 INFO @ Sat, 11 Dec 2021 15:47:56: 20000000 INFO @ Sat, 11 Dec 2021 15:47:57: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 15:47:57: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 15:47:57: #1 total tags in treatment: 9702184 INFO @ Sat, 11 Dec 2021 15:47:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:47:57: #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 15:47:57: #1 tags after filtering in treatment: 8400089 INFO @ Sat, 11 Dec 2021 15:47:57: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 15:47:57: #1 finished! INFO @ Sat, 11 Dec 2021 15:47:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:47:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:47:58: #2 number of paired peaks: 6512 INFO @ Sat, 11 Dec 2021 15:47:58: start model_add_line... INFO @ Sat, 11 Dec 2021 15:47:58: start X-correlation... INFO @ Sat, 11 Dec 2021 15:47:58: end of X-cor INFO @ Sat, 11 Dec 2021 15:47:58: #2 finished! INFO @ Sat, 11 Dec 2021 15:47:58: #2 predicted fragment length is 177 bps INFO @ Sat, 11 Dec 2021 15:47:58: #2 alternative fragment length(s) may be 177 bps INFO @ Sat, 11 Dec 2021 15:47:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.05_model.r INFO @ Sat, 11 Dec 2021 15:47:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:47:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:47:59: 14000000 INFO @ Sat, 11 Dec 2021 15:48:02: 19000000 INFO @ Sat, 11 Dec 2021 15:48:05: 15000000 INFO @ Sat, 11 Dec 2021 15:48:08: 20000000 INFO @ Sat, 11 Dec 2021 15:48:09: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 15:48:09: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 15:48:09: #1 total tags in treatment: 9702184 INFO @ Sat, 11 Dec 2021 15:48:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:48:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:48:09: #1 tags after filtering in treatment: 8400089 INFO @ Sat, 11 Dec 2021 15:48:09: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 15:48:09: #1 finished! INFO @ Sat, 11 Dec 2021 15:48:09: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:48:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:48:10: #2 number of paired peaks: 6512 INFO @ Sat, 11 Dec 2021 15:48:10: start model_add_line... INFO @ Sat, 11 Dec 2021 15:48:10: start X-correlation... INFO @ Sat, 11 Dec 2021 15:48:10: end of X-cor INFO @ Sat, 11 Dec 2021 15:48:10: #2 finished! INFO @ Sat, 11 Dec 2021 15:48:10: #2 predicted fragment length is 177 bps INFO @ Sat, 11 Dec 2021 15:48:10: #2 alternative fragment length(s) may be 177 bps INFO @ Sat, 11 Dec 2021 15:48:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.10_model.r INFO @ Sat, 11 Dec 2021 15:48:10: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:48:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:48:11: 16000000 INFO @ Sat, 11 Dec 2021 15:48:17: 17000000 INFO @ Sat, 11 Dec 2021 15:48:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:48:23: 18000000 INFO @ Sat, 11 Dec 2021 15:48:29: 19000000 INFO @ Sat, 11 Dec 2021 15:48:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:48:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:48:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.05_summits.bed INFO @ Sat, 11 Dec 2021 15:48:32: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8363 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:48:33: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:48:35: 20000000 INFO @ Sat, 11 Dec 2021 15:48:35: #1 tag size is determined as 42 bps INFO @ Sat, 11 Dec 2021 15:48:35: #1 tag size = 42 INFO @ Sat, 11 Dec 2021 15:48:35: #1 total tags in treatment: 9702184 INFO @ Sat, 11 Dec 2021 15:48:35: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:48:35: #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 15:48:35: #1 tags after filtering in treatment: 8400089 INFO @ Sat, 11 Dec 2021 15:48:35: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 11 Dec 2021 15:48:35: #1 finished! INFO @ Sat, 11 Dec 2021 15:48:35: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:48:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:48:36: #2 number of paired peaks: 6512 INFO @ Sat, 11 Dec 2021 15:48:36: start model_add_line... INFO @ Sat, 11 Dec 2021 15:48:36: start X-correlation... INFO @ Sat, 11 Dec 2021 15:48:36: end of X-cor INFO @ Sat, 11 Dec 2021 15:48:36: #2 finished! INFO @ Sat, 11 Dec 2021 15:48:36: #2 predicted fragment length is 177 bps INFO @ Sat, 11 Dec 2021 15:48:36: #2 alternative fragment length(s) may be 177 bps INFO @ Sat, 11 Dec 2021 15:48:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.20_model.r INFO @ Sat, 11 Dec 2021 15:48:36: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:48:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:48:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:48:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:48:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.10_summits.bed INFO @ Sat, 11 Dec 2021 15:48:44: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5586 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:49:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:49:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:49:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:49:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7628882/SRX7628882.20_summits.bed INFO @ Sat, 11 Dec 2021 15:49:11: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (3003 records, 4 fields): 20 millis CompletedMACS2peakCalling