Job ID = 14167699 SRX = SRX4712966 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:24 22664022 reads; of these: 22664022 (100.00%) were unpaired; of these: 1594112 (7.03%) aligned 0 times 11017672 (48.61%) aligned exactly 1 time 10052238 (44.35%) aligned >1 times 92.97% overall alignment rate Time searching: 00:11:25 Overall time: 00:11:25 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 9284199 / 21069910 = 0.4406 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 13:24:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.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 13:24:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:24:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:24:24: 1000000 INFO @ Fri, 10 Dec 2021 13:24:29: 2000000 INFO @ Fri, 10 Dec 2021 13:24:34: 3000000 INFO @ Fri, 10 Dec 2021 13:24:39: 4000000 INFO @ Fri, 10 Dec 2021 13:24:44: 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 13:24:49: 6000000 INFO @ Fri, 10 Dec 2021 13:24:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.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 13:24:49: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:24:49: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:24:55: 7000000 INFO @ Fri, 10 Dec 2021 13:24:57: 1000000 INFO @ Fri, 10 Dec 2021 13:25:00: 8000000 INFO @ Fri, 10 Dec 2021 13:25:04: 2000000 INFO @ Fri, 10 Dec 2021 13:25:06: 9000000 INFO @ Fri, 10 Dec 2021 13:25:11: 3000000 INFO @ Fri, 10 Dec 2021 13:25:11: 10000000 INFO @ Fri, 10 Dec 2021 13:25:17: 11000000 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 13:25:19: 4000000 INFO @ Fri, 10 Dec 2021 13:25:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.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 13:25:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 13:25:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 13:25:21: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 13:25:21: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 13:25:21: #1 total tags in treatment: 11785711 INFO @ Fri, 10 Dec 2021 13:25:21: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:25:21: #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 13:25:22: #1 tags after filtering in treatment: 11785687 INFO @ Fri, 10 Dec 2021 13:25:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:25:22: #1 finished! INFO @ Fri, 10 Dec 2021 13:25:22: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:25:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:25:23: #2 number of paired peaks: 825 WARNING @ Fri, 10 Dec 2021 13:25:23: Fewer paired peaks (825) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 825 pairs to build model! INFO @ Fri, 10 Dec 2021 13:25:23: start model_add_line... INFO @ Fri, 10 Dec 2021 13:25:23: start X-correlation... INFO @ Fri, 10 Dec 2021 13:25:23: end of X-cor INFO @ Fri, 10 Dec 2021 13:25:23: #2 finished! INFO @ Fri, 10 Dec 2021 13:25:23: #2 predicted fragment length is 115 bps INFO @ Fri, 10 Dec 2021 13:25:23: #2 alternative fragment length(s) may be 115 bps INFO @ Fri, 10 Dec 2021 13:25:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.05_model.r INFO @ Fri, 10 Dec 2021 13:25:23: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:25:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:25:25: 1000000 INFO @ Fri, 10 Dec 2021 13:25:26: 5000000 INFO @ Fri, 10 Dec 2021 13:25:30: 2000000 INFO @ Fri, 10 Dec 2021 13:25:33: 6000000 INFO @ Fri, 10 Dec 2021 13:25:36: 3000000 INFO @ Fri, 10 Dec 2021 13:25:40: 7000000 INFO @ Fri, 10 Dec 2021 13:25:41: 4000000 INFO @ Fri, 10 Dec 2021 13:25:47: 5000000 INFO @ Fri, 10 Dec 2021 13:25:48: 8000000 INFO @ Fri, 10 Dec 2021 13:25:49: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:25:52: 6000000 INFO @ Fri, 10 Dec 2021 13:25:55: 9000000 INFO @ Fri, 10 Dec 2021 13:25:58: 7000000 INFO @ Fri, 10 Dec 2021 13:26:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.05_peaks.xls INFO @ Fri, 10 Dec 2021 13:26:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:26:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.05_summits.bed INFO @ Fri, 10 Dec 2021 13:26:03: Done! INFO @ Fri, 10 Dec 2021 13:26:03: 10000000 pass1 - making usageList (761 chroms): 3 millis pass2 - checking and writing primary data (11500 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 13:26:03: 8000000 INFO @ Fri, 10 Dec 2021 13:26:09: 9000000 INFO @ Fri, 10 Dec 2021 13:26:10: 11000000 INFO @ Fri, 10 Dec 2021 13:26:15: 10000000 INFO @ Fri, 10 Dec 2021 13:26:16: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 13:26:16: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 13:26:16: #1 total tags in treatment: 11785711 INFO @ Fri, 10 Dec 2021 13:26:16: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:26:16: #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 13:26:16: #1 tags after filtering in treatment: 11785687 INFO @ Fri, 10 Dec 2021 13:26:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:26:16: #1 finished! INFO @ Fri, 10 Dec 2021 13:26:16: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:26:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:26:18: #2 number of paired peaks: 825 WARNING @ Fri, 10 Dec 2021 13:26:18: Fewer paired peaks (825) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 825 pairs to build model! INFO @ Fri, 10 Dec 2021 13:26:18: start model_add_line... INFO @ Fri, 10 Dec 2021 13:26:18: start X-correlation... INFO @ Fri, 10 Dec 2021 13:26:18: end of X-cor INFO @ Fri, 10 Dec 2021 13:26:18: #2 finished! INFO @ Fri, 10 Dec 2021 13:26:18: #2 predicted fragment length is 115 bps INFO @ Fri, 10 Dec 2021 13:26:18: #2 alternative fragment length(s) may be 115 bps INFO @ Fri, 10 Dec 2021 13:26:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.10_model.r INFO @ Fri, 10 Dec 2021 13:26:18: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:26:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:26:20: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 13:26:24: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 13:26:24: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 13:26:24: #1 total tags in treatment: 11785711 INFO @ Fri, 10 Dec 2021 13:26:24: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 13:26:24: #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 13:26:24: #1 tags after filtering in treatment: 11785687 INFO @ Fri, 10 Dec 2021 13:26:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 13:26:24: #1 finished! INFO @ Fri, 10 Dec 2021 13:26:24: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 13:26:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 13:26:25: #2 number of paired peaks: 825 WARNING @ Fri, 10 Dec 2021 13:26:25: Fewer paired peaks (825) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 825 pairs to build model! INFO @ Fri, 10 Dec 2021 13:26:25: start model_add_line... INFO @ Fri, 10 Dec 2021 13:26:25: start X-correlation... INFO @ Fri, 10 Dec 2021 13:26:25: end of X-cor INFO @ Fri, 10 Dec 2021 13:26:25: #2 finished! INFO @ Fri, 10 Dec 2021 13:26:25: #2 predicted fragment length is 115 bps INFO @ Fri, 10 Dec 2021 13:26:25: #2 alternative fragment length(s) may be 115 bps INFO @ Fri, 10 Dec 2021 13:26:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.20_model.r INFO @ Fri, 10 Dec 2021 13:26:25: #3 Call peaks... INFO @ Fri, 10 Dec 2021 13:26:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 13:26:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 13:26:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 13:27:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.10_peaks.xls INFO @ Fri, 10 Dec 2021 13:27:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:27:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.10_summits.bed INFO @ Fri, 10 Dec 2021 13:27:04: Done! INFO @ Fri, 10 Dec 2021 13:27:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.20_peaks.xls INFO @ Fri, 10 Dec 2021 13:27:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 13:27:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4712966/SRX4712966.20_summits.bed INFO @ Fri, 10 Dec 2021 13:27:04: Done! pass1 - making usageList (617 chroms): 3 millis pass2 - checking and writing primary data (5502 records, 4 fields): 28 millis CompletedMACS2peakCalling pass1 - making usageList (496 chroms): 2 millis pass2 - checking and writing primary data (2486 records, 4 fields): 15 millis CompletedMACS2peakCalling