Job ID = 14167124 SRX = SRX4712946 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 24841699 spots for SRR7874076/SRR7874076.sra Written 24841699 spots for SRR7874076/SRR7874076.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167576 ("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: 00:06:40 24841699 reads; of these: 24841699 (100.00%) were unpaired; of these: 1416602 (5.70%) aligned 0 times 17970937 (72.34%) aligned exactly 1 time 5454160 (21.96%) aligned >1 times 94.30% overall alignment rate Time searching: 00:06:40 Overall time: 00:06:40 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_rmdupse_core] 8410100 / 23425097 = 0.3590 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 10:26:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.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 10:26:41: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:26:41: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:26:46: 1000000 INFO @ Fri, 10 Dec 2021 10:26:51: 2000000 INFO @ Fri, 10 Dec 2021 10:26:56: 3000000 INFO @ Fri, 10 Dec 2021 10:27:01: 4000000 INFO @ Fri, 10 Dec 2021 10:27:06: 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 10:27:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.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 10:27:11: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:27:11: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:27:11: 6000000 INFO @ Fri, 10 Dec 2021 10:27:17: 7000000 INFO @ Fri, 10 Dec 2021 10:27:17: 1000000 INFO @ Fri, 10 Dec 2021 10:27:23: 8000000 INFO @ Fri, 10 Dec 2021 10:27:24: 2000000 INFO @ Fri, 10 Dec 2021 10:27:29: 9000000 INFO @ Fri, 10 Dec 2021 10:27:31: 3000000 INFO @ Fri, 10 Dec 2021 10:27:35: 10000000 INFO @ Fri, 10 Dec 2021 10:27:38: 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 10:27:40: 11000000 INFO @ Fri, 10 Dec 2021 10:27:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.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 10:27:41: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:27:41: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:27:45: 5000000 INFO @ Fri, 10 Dec 2021 10:27:46: 12000000 INFO @ Fri, 10 Dec 2021 10:27:46: 1000000 INFO @ Fri, 10 Dec 2021 10:27:52: 6000000 INFO @ Fri, 10 Dec 2021 10:27:52: 2000000 INFO @ Fri, 10 Dec 2021 10:27:52: 13000000 INFO @ Fri, 10 Dec 2021 10:27:58: 14000000 INFO @ Fri, 10 Dec 2021 10:27:58: 3000000 INFO @ Fri, 10 Dec 2021 10:27:59: 7000000 INFO @ Fri, 10 Dec 2021 10:28:04: 15000000 INFO @ Fri, 10 Dec 2021 10:28:04: 4000000 INFO @ Fri, 10 Dec 2021 10:28:05: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:28:05: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:28:05: #1 total tags in treatment: 15014997 INFO @ Fri, 10 Dec 2021 10:28:05: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:28:05: #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 10:28:05: #1 tags after filtering in treatment: 15014997 INFO @ Fri, 10 Dec 2021 10:28:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:28:05: #1 finished! INFO @ Fri, 10 Dec 2021 10:28:05: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:28:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:28:06: 8000000 INFO @ Fri, 10 Dec 2021 10:28:06: #2 number of paired peaks: 479 WARNING @ Fri, 10 Dec 2021 10:28:06: Fewer paired peaks (479) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 479 pairs to build model! INFO @ Fri, 10 Dec 2021 10:28:06: start model_add_line... INFO @ Fri, 10 Dec 2021 10:28:06: start X-correlation... INFO @ Fri, 10 Dec 2021 10:28:06: end of X-cor INFO @ Fri, 10 Dec 2021 10:28:06: #2 finished! INFO @ Fri, 10 Dec 2021 10:28:06: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Dec 2021 10:28:06: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 10 Dec 2021 10:28:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.05_model.r INFO @ Fri, 10 Dec 2021 10:28:06: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:28:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:28:10: 5000000 INFO @ Fri, 10 Dec 2021 10:28:12: 9000000 INFO @ Fri, 10 Dec 2021 10:28:16: 6000000 INFO @ Fri, 10 Dec 2021 10:28:19: 10000000 INFO @ Fri, 10 Dec 2021 10:28:22: 7000000 INFO @ Fri, 10 Dec 2021 10:28:26: 11000000 INFO @ Fri, 10 Dec 2021 10:28:28: 8000000 INFO @ Fri, 10 Dec 2021 10:28:33: 12000000 INFO @ Fri, 10 Dec 2021 10:28:34: 9000000 INFO @ Fri, 10 Dec 2021 10:28:35: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:28:40: 13000000 INFO @ Fri, 10 Dec 2021 10:28:40: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:28:46: 11000000 INFO @ Fri, 10 Dec 2021 10:28:47: 14000000 INFO @ Fri, 10 Dec 2021 10:28:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:28:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:28:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.05_summits.bed INFO @ Fri, 10 Dec 2021 10:28:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7250 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:28:52: 12000000 INFO @ Fri, 10 Dec 2021 10:28:54: 15000000 INFO @ Fri, 10 Dec 2021 10:28:54: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:28:54: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:28:54: #1 total tags in treatment: 15014997 INFO @ Fri, 10 Dec 2021 10:28:54: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:28:54: #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 10:28:54: #1 tags after filtering in treatment: 15014997 INFO @ Fri, 10 Dec 2021 10:28:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:28:54: #1 finished! INFO @ Fri, 10 Dec 2021 10:28:54: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:28:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:28:55: #2 number of paired peaks: 479 WARNING @ Fri, 10 Dec 2021 10:28:55: Fewer paired peaks (479) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 479 pairs to build model! INFO @ Fri, 10 Dec 2021 10:28:55: start model_add_line... INFO @ Fri, 10 Dec 2021 10:28:55: start X-correlation... INFO @ Fri, 10 Dec 2021 10:28:55: end of X-cor INFO @ Fri, 10 Dec 2021 10:28:55: #2 finished! INFO @ Fri, 10 Dec 2021 10:28:55: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Dec 2021 10:28:55: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 10 Dec 2021 10:28:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.10_model.r INFO @ Fri, 10 Dec 2021 10:28:55: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:28:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:28:58: 13000000 INFO @ Fri, 10 Dec 2021 10:29:03: 14000000 INFO @ Fri, 10 Dec 2021 10:29:08: 15000000 INFO @ Fri, 10 Dec 2021 10:29:09: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:29:09: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:29:09: #1 total tags in treatment: 15014997 INFO @ Fri, 10 Dec 2021 10:29:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:29:09: #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 10:29:09: #1 tags after filtering in treatment: 15014997 INFO @ Fri, 10 Dec 2021 10:29:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:29:09: #1 finished! INFO @ Fri, 10 Dec 2021 10:29:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:29:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:29:10: #2 number of paired peaks: 479 WARNING @ Fri, 10 Dec 2021 10:29:10: Fewer paired peaks (479) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 479 pairs to build model! INFO @ Fri, 10 Dec 2021 10:29:10: start model_add_line... INFO @ Fri, 10 Dec 2021 10:29:10: start X-correlation... INFO @ Fri, 10 Dec 2021 10:29:10: end of X-cor INFO @ Fri, 10 Dec 2021 10:29:10: #2 finished! INFO @ Fri, 10 Dec 2021 10:29:10: #2 predicted fragment length is 155 bps INFO @ Fri, 10 Dec 2021 10:29:10: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 10 Dec 2021 10:29:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.20_model.r INFO @ Fri, 10 Dec 2021 10:29:10: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:29:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:29:24: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:29:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:29:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:29:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.10_summits.bed INFO @ Fri, 10 Dec 2021 10:29:39: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5570 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:29:39: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:29:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:29:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:29:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712946/SRX4712946.20_summits.bed INFO @ Fri, 10 Dec 2021 10:29:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3878 records, 4 fields): 6 millis CompletedMACS2peakCalling