Job ID = 14167336 SRX = SRX7723717 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: 00:07:09 22112553 reads; of these: 22112553 (100.00%) were unpaired; of these: 7098809 (32.10%) aligned 0 times 10834530 (49.00%) aligned exactly 1 time 4179214 (18.90%) aligned >1 times 67.90% overall alignment rate Time searching: 00:07:09 Overall time: 00:07:09 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 8 files... [bam_rmdupse_core] 5208262 / 15013744 = 0.3469 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 12:03:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.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 12:03:51: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:03:51: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:04:01: 1000000 INFO @ Fri, 10 Dec 2021 12:04:12: 2000000 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 12:04:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.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 12:04:21: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:04:21: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:04:22: 3000000 INFO @ Fri, 10 Dec 2021 12:04:32: 1000000 INFO @ Fri, 10 Dec 2021 12:04:33: 4000000 INFO @ Fri, 10 Dec 2021 12:04:41: 2000000 INFO @ Fri, 10 Dec 2021 12:04:42: 5000000 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 12:04:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.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 12:04:50: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:04:50: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:04:51: 3000000 INFO @ Fri, 10 Dec 2021 12:04:52: 6000000 INFO @ Fri, 10 Dec 2021 12:04:58: 1000000 INFO @ Fri, 10 Dec 2021 12:05:00: 4000000 INFO @ Fri, 10 Dec 2021 12:05:01: 7000000 INFO @ Fri, 10 Dec 2021 12:05:07: 2000000 INFO @ Fri, 10 Dec 2021 12:05:09: 5000000 INFO @ Fri, 10 Dec 2021 12:05:11: 8000000 INFO @ Fri, 10 Dec 2021 12:05:15: 3000000 INFO @ Fri, 10 Dec 2021 12:05:18: 6000000 INFO @ Fri, 10 Dec 2021 12:05:21: 9000000 INFO @ Fri, 10 Dec 2021 12:05:24: 4000000 INFO @ Fri, 10 Dec 2021 12:05:28: 7000000 INFO @ Fri, 10 Dec 2021 12:05:28: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 12:05:28: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 12:05:28: #1 total tags in treatment: 9805482 INFO @ Fri, 10 Dec 2021 12:05:28: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:05:28: #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 12:05:29: #1 tags after filtering in treatment: 9805334 INFO @ Fri, 10 Dec 2021 12:05:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:05:29: #1 finished! INFO @ Fri, 10 Dec 2021 12:05:29: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:05:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:05:29: #2 number of paired peaks: 1187 INFO @ Fri, 10 Dec 2021 12:05:29: start model_add_line... INFO @ Fri, 10 Dec 2021 12:05:29: start X-correlation... INFO @ Fri, 10 Dec 2021 12:05:29: end of X-cor INFO @ Fri, 10 Dec 2021 12:05:29: #2 finished! INFO @ Fri, 10 Dec 2021 12:05:29: #2 predicted fragment length is 69 bps INFO @ Fri, 10 Dec 2021 12:05:29: #2 alternative fragment length(s) may be 4,69 bps INFO @ Fri, 10 Dec 2021 12:05:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.05_model.r WARNING @ Fri, 10 Dec 2021 12:05:29: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:05:29: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Fri, 10 Dec 2021 12:05:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:05:29: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:05:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:05:33: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:05:37: 8000000 INFO @ Fri, 10 Dec 2021 12:05:41: 6000000 INFO @ Fri, 10 Dec 2021 12:05:46: 9000000 INFO @ Fri, 10 Dec 2021 12:05:49: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:05:50: 7000000 INFO @ Fri, 10 Dec 2021 12:05:53: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 12:05:53: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 12:05:53: #1 total tags in treatment: 9805482 INFO @ Fri, 10 Dec 2021 12:05:53: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:05:53: #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 12:05:54: #1 tags after filtering in treatment: 9805334 INFO @ Fri, 10 Dec 2021 12:05:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:05:54: #1 finished! INFO @ Fri, 10 Dec 2021 12:05:54: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:05:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:05:55: #2 number of paired peaks: 1187 INFO @ Fri, 10 Dec 2021 12:05:55: start model_add_line... INFO @ Fri, 10 Dec 2021 12:05:55: start X-correlation... INFO @ Fri, 10 Dec 2021 12:05:55: end of X-cor INFO @ Fri, 10 Dec 2021 12:05:55: #2 finished! INFO @ Fri, 10 Dec 2021 12:05:55: #2 predicted fragment length is 69 bps INFO @ Fri, 10 Dec 2021 12:05:55: #2 alternative fragment length(s) may be 4,69 bps INFO @ Fri, 10 Dec 2021 12:05:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.10_model.r WARNING @ Fri, 10 Dec 2021 12:05:55: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:05:55: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Fri, 10 Dec 2021 12:05:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:05:55: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:05:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:05:57: 8000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:05:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:05:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:05:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.05_summits.bed INFO @ Fri, 10 Dec 2021 12:05:58: Done! pass1 - making usageList (662 chroms): 1 millis pass2 - checking and writing primary data (2295 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:06:04: 9000000 INFO @ Fri, 10 Dec 2021 12:06:09: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 12:06:09: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 12:06:09: #1 total tags in treatment: 9805482 INFO @ Fri, 10 Dec 2021 12:06:09: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:06:09: #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 12:06:09: #1 tags after filtering in treatment: 9805334 INFO @ Fri, 10 Dec 2021 12:06:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:06:09: #1 finished! INFO @ Fri, 10 Dec 2021 12:06:09: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:06:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:06:10: #2 number of paired peaks: 1187 INFO @ Fri, 10 Dec 2021 12:06:10: start model_add_line... INFO @ Fri, 10 Dec 2021 12:06:10: start X-correlation... INFO @ Fri, 10 Dec 2021 12:06:10: end of X-cor INFO @ Fri, 10 Dec 2021 12:06:10: #2 finished! INFO @ Fri, 10 Dec 2021 12:06:10: #2 predicted fragment length is 69 bps INFO @ Fri, 10 Dec 2021 12:06:10: #2 alternative fragment length(s) may be 4,69 bps INFO @ Fri, 10 Dec 2021 12:06:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.20_model.r WARNING @ Fri, 10 Dec 2021 12:06:10: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:06:10: #2 You may need to consider one of the other alternative d(s): 4,69 WARNING @ Fri, 10 Dec 2021 12:06:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:06:10: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:06:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:06:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:06:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:06:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:06:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.10_summits.bed INFO @ Fri, 10 Dec 2021 12:06:24: Done! pass1 - making usageList (590 chroms): 2 millis pass2 - checking and writing primary data (1846 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:06:30: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:06:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:06:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:06:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7723717/SRX7723717.20_summits.bed INFO @ Fri, 10 Dec 2021 12:06:39: Done! pass1 - making usageList (501 chroms): 1 millis pass2 - checking and writing primary data (1293 records, 4 fields): 15 millis CompletedMACS2peakCalling