Job ID = 14167136 SRX = SRX4712952 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 45849454 spots for SRR7874082/SRR7874082.sra Written 45849454 spots for SRR7874082/SRR7874082.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167635 ("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: 00:13:33 45849454 reads; of these: 45849454 (100.00%) were unpaired; of these: 2353678 (5.13%) aligned 0 times 33583453 (73.25%) aligned exactly 1 time 9912323 (21.62%) aligned >1 times 94.87% overall alignment rate Time searching: 00:13:33 Overall time: 00:13:33 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 20 files... [bam_rmdupse_core] 27329453 / 43495776 = 0.6283 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 10:44:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.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 10:44:35: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:44:35: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:44:40: 1000000 INFO @ Fri, 10 Dec 2021 10:44:45: 2000000 INFO @ Fri, 10 Dec 2021 10:44:50: 3000000 INFO @ Fri, 10 Dec 2021 10:44:55: 4000000 INFO @ Fri, 10 Dec 2021 10:45:01: 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 @ Fri, 10 Dec 2021 10:45:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.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 10:45:05: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:45:05: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:45:06: 6000000 INFO @ Fri, 10 Dec 2021 10:45:11: 1000000 INFO @ Fri, 10 Dec 2021 10:45:11: 7000000 INFO @ Fri, 10 Dec 2021 10:45:17: 2000000 INFO @ Fri, 10 Dec 2021 10:45:17: 8000000 INFO @ Fri, 10 Dec 2021 10:45:22: 3000000 INFO @ Fri, 10 Dec 2021 10:45:23: 9000000 INFO @ Fri, 10 Dec 2021 10:45:28: 4000000 INFO @ Fri, 10 Dec 2021 10:45:28: 10000000 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 10:45:34: 5000000 INFO @ Fri, 10 Dec 2021 10:45:34: 11000000 INFO @ Fri, 10 Dec 2021 10:45:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.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 10:45:35: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:45:35: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:45:40: 6000000 INFO @ Fri, 10 Dec 2021 10:45:40: 12000000 INFO @ Fri, 10 Dec 2021 10:45:42: 1000000 INFO @ Fri, 10 Dec 2021 10:45:46: 7000000 INFO @ Fri, 10 Dec 2021 10:45:46: 13000000 INFO @ Fri, 10 Dec 2021 10:45:48: 2000000 INFO @ Fri, 10 Dec 2021 10:45:52: 8000000 INFO @ Fri, 10 Dec 2021 10:45:52: 14000000 INFO @ Fri, 10 Dec 2021 10:45:54: 3000000 INFO @ Fri, 10 Dec 2021 10:45:58: 9000000 INFO @ Fri, 10 Dec 2021 10:45:58: 15000000 INFO @ Fri, 10 Dec 2021 10:46:00: 4000000 INFO @ Fri, 10 Dec 2021 10:46:04: 10000000 INFO @ Fri, 10 Dec 2021 10:46:04: 16000000 INFO @ Fri, 10 Dec 2021 10:46:05: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:46:05: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:46:05: #1 total tags in treatment: 16166323 INFO @ Fri, 10 Dec 2021 10:46:05: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:46:05: #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 10:46:05: #1 tags after filtering in treatment: 16166323 INFO @ Fri, 10 Dec 2021 10:46:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:46:05: #1 finished! INFO @ Fri, 10 Dec 2021 10:46:05: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:46:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:46:06: 5000000 INFO @ Fri, 10 Dec 2021 10:46:06: #2 number of paired peaks: 460 WARNING @ Fri, 10 Dec 2021 10:46:06: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Fri, 10 Dec 2021 10:46:06: start model_add_line... INFO @ Fri, 10 Dec 2021 10:46:06: start X-correlation... INFO @ Fri, 10 Dec 2021 10:46:06: end of X-cor INFO @ Fri, 10 Dec 2021 10:46:06: #2 finished! INFO @ Fri, 10 Dec 2021 10:46:06: #2 predicted fragment length is 128 bps INFO @ Fri, 10 Dec 2021 10:46:06: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 10 Dec 2021 10:46:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.05_model.r INFO @ Fri, 10 Dec 2021 10:46:06: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:46:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:46:10: 11000000 INFO @ Fri, 10 Dec 2021 10:46:12: 6000000 INFO @ Fri, 10 Dec 2021 10:46:16: 12000000 INFO @ Fri, 10 Dec 2021 10:46:19: 7000000 INFO @ Fri, 10 Dec 2021 10:46:22: 13000000 INFO @ Fri, 10 Dec 2021 10:46:25: 8000000 INFO @ Fri, 10 Dec 2021 10:46:28: 14000000 INFO @ Fri, 10 Dec 2021 10:46:32: 9000000 INFO @ Fri, 10 Dec 2021 10:46:34: 15000000 INFO @ Fri, 10 Dec 2021 10:46:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:46:39: 10000000 INFO @ Fri, 10 Dec 2021 10:46:41: 16000000 INFO @ Fri, 10 Dec 2021 10:46:42: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:46:42: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:46:42: #1 total tags in treatment: 16166323 INFO @ Fri, 10 Dec 2021 10:46:42: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:46:42: #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 10:46:42: #1 tags after filtering in treatment: 16166323 INFO @ Fri, 10 Dec 2021 10:46:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:46:42: #1 finished! INFO @ Fri, 10 Dec 2021 10:46:42: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:46:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:46:43: #2 number of paired peaks: 460 WARNING @ Fri, 10 Dec 2021 10:46:43: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Fri, 10 Dec 2021 10:46:43: start model_add_line... INFO @ Fri, 10 Dec 2021 10:46:43: start X-correlation... INFO @ Fri, 10 Dec 2021 10:46:43: end of X-cor INFO @ Fri, 10 Dec 2021 10:46:43: #2 finished! INFO @ Fri, 10 Dec 2021 10:46:43: #2 predicted fragment length is 128 bps INFO @ Fri, 10 Dec 2021 10:46:43: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 10 Dec 2021 10:46:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.10_model.r INFO @ Fri, 10 Dec 2021 10:46:43: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:46:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:46:44: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:46:50: 12000000 INFO @ Fri, 10 Dec 2021 10:46:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:46:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:46:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.05_summits.bed INFO @ Fri, 10 Dec 2021 10:46:53: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8032 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:46:56: 13000000 INFO @ Fri, 10 Dec 2021 10:47:03: 14000000 INFO @ Fri, 10 Dec 2021 10:47:09: 15000000 INFO @ Fri, 10 Dec 2021 10:47:15: 16000000 INFO @ Fri, 10 Dec 2021 10:47:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:47:16: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:47:16: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:47:16: #1 total tags in treatment: 16166323 INFO @ Fri, 10 Dec 2021 10:47:16: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:47:16: #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 10:47:16: #1 tags after filtering in treatment: 16166323 INFO @ Fri, 10 Dec 2021 10:47:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:47:16: #1 finished! INFO @ Fri, 10 Dec 2021 10:47:16: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:47:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:47:17: #2 number of paired peaks: 460 WARNING @ Fri, 10 Dec 2021 10:47:17: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Fri, 10 Dec 2021 10:47:17: start model_add_line... INFO @ Fri, 10 Dec 2021 10:47:17: start X-correlation... INFO @ Fri, 10 Dec 2021 10:47:18: end of X-cor INFO @ Fri, 10 Dec 2021 10:47:18: #2 finished! INFO @ Fri, 10 Dec 2021 10:47:18: #2 predicted fragment length is 128 bps INFO @ Fri, 10 Dec 2021 10:47:18: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 10 Dec 2021 10:47:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.20_model.r INFO @ Fri, 10 Dec 2021 10:47:18: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:47:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:47:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:47:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:47:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.10_summits.bed INFO @ Fri, 10 Dec 2021 10:47:31: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5368 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:47:51: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:48:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:48:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:48:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712952/SRX4712952.20_summits.bed INFO @ Fri, 10 Dec 2021 10:48:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3585 records, 4 fields): 4 millis CompletedMACS2peakCalling