Job ID = 14172708 SRX = SRX9427699 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:35 21581221 reads; of these: 21581221 (100.00%) were unpaired; of these: 9481002 (43.93%) aligned 0 times 3874091 (17.95%) aligned exactly 1 time 8226128 (38.12%) aligned >1 times 56.07% overall alignment rate Time searching: 00:07:36 Overall time: 00:07:36 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] 4573565 / 12100219 = 0.3780 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 16:51:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.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 16:51:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:51:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:51:28: 1000000 INFO @ Sat, 11 Dec 2021 16:51:35: 2000000 INFO @ Sat, 11 Dec 2021 16:51:42: 3000000 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 16:51:49: 4000000 INFO @ Sat, 11 Dec 2021 16:51:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.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 16:51:50: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:51:50: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:51:57: 5000000 INFO @ Sat, 11 Dec 2021 16:51:57: 1000000 INFO @ Sat, 11 Dec 2021 16:52:04: 2000000 INFO @ Sat, 11 Dec 2021 16:52:05: 6000000 INFO @ Sat, 11 Dec 2021 16:52:10: 3000000 INFO @ Sat, 11 Dec 2021 16:52:12: 7000000 INFO @ Sat, 11 Dec 2021 16:52:16: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 16:52:16: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 16:52:16: #1 total tags in treatment: 7526654 INFO @ Sat, 11 Dec 2021 16:52:16: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:52:16: #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 16:52:16: 4000000 INFO @ Sat, 11 Dec 2021 16:52:17: #1 tags after filtering in treatment: 7526643 INFO @ Sat, 11 Dec 2021 16:52:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 16:52:17: #1 finished! INFO @ Sat, 11 Dec 2021 16:52:17: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:52:17: #2 looking for paired plus/minus strand peaks... 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 16:52:18: #2 number of paired peaks: 5538 INFO @ Sat, 11 Dec 2021 16:52:18: start model_add_line... INFO @ Sat, 11 Dec 2021 16:52:19: start X-correlation... INFO @ Sat, 11 Dec 2021 16:52:19: end of X-cor INFO @ Sat, 11 Dec 2021 16:52:19: #2 finished! INFO @ Sat, 11 Dec 2021 16:52:19: #2 predicted fragment length is 54 bps INFO @ Sat, 11 Dec 2021 16:52:19: #2 alternative fragment length(s) may be 3,54 bps INFO @ Sat, 11 Dec 2021 16:52:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.05_model.r WARNING @ Sat, 11 Dec 2021 16:52:19: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 16:52:19: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Sat, 11 Dec 2021 16:52:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 16:52:19: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:52:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:52:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.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 16:52:21: #1 read tag files... INFO @ Sat, 11 Dec 2021 16:52:21: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 16:52:23: 5000000 INFO @ Sat, 11 Dec 2021 16:52:28: 1000000 INFO @ Sat, 11 Dec 2021 16:52:31: 6000000 INFO @ Sat, 11 Dec 2021 16:52:35: 2000000 INFO @ Sat, 11 Dec 2021 16:52:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:52:39: 7000000 INFO @ Sat, 11 Dec 2021 16:52:42: 3000000 INFO @ Sat, 11 Dec 2021 16:52:42: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 16:52:42: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 16:52:42: #1 total tags in treatment: 7526654 INFO @ Sat, 11 Dec 2021 16:52:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:52:42: #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 16:52:43: #1 tags after filtering in treatment: 7526643 INFO @ Sat, 11 Dec 2021 16:52:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 16:52:43: #1 finished! INFO @ Sat, 11 Dec 2021 16:52:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:52:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:52:44: #2 number of paired peaks: 5538 INFO @ Sat, 11 Dec 2021 16:52:44: start model_add_line... INFO @ Sat, 11 Dec 2021 16:52:45: start X-correlation... INFO @ Sat, 11 Dec 2021 16:52:45: end of X-cor INFO @ Sat, 11 Dec 2021 16:52:45: #2 finished! INFO @ Sat, 11 Dec 2021 16:52:45: #2 predicted fragment length is 54 bps INFO @ Sat, 11 Dec 2021 16:52:45: #2 alternative fragment length(s) may be 3,54 bps INFO @ Sat, 11 Dec 2021 16:52:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.10_model.r WARNING @ Sat, 11 Dec 2021 16:52:45: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 16:52:45: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Sat, 11 Dec 2021 16:52:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 16:52:45: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:52:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 16:52:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.05_peaks.xls INFO @ Sat, 11 Dec 2021 16:52:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:52:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.05_summits.bed INFO @ Sat, 11 Dec 2021 16:52:46: Done! pass1 - making usageList (1112 chroms): 3 millis pass2 - checking and writing primary data (5698 records, 4 fields): 76 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:52:48: 4000000 INFO @ Sat, 11 Dec 2021 16:52:55: 5000000 INFO @ Sat, 11 Dec 2021 16:53:02: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 16:53:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:53:09: 7000000 INFO @ Sat, 11 Dec 2021 16:53:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.10_peaks.xls INFO @ Sat, 11 Dec 2021 16:53:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:53:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.10_summits.bed INFO @ Sat, 11 Dec 2021 16:53:12: Done! pass1 - making usageList (954 chroms): 3 millis pass2 - checking and writing primary data (3388 records, 4 fields): 63 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 16:53:13: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 16:53:13: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 16:53:13: #1 total tags in treatment: 7526654 INFO @ Sat, 11 Dec 2021 16:53:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 16:53:13: #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 16:53:14: #1 tags after filtering in treatment: 7526643 INFO @ Sat, 11 Dec 2021 16:53:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 16:53:14: #1 finished! INFO @ Sat, 11 Dec 2021 16:53:14: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 16:53:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 16:53:15: #2 number of paired peaks: 5538 INFO @ Sat, 11 Dec 2021 16:53:15: start model_add_line... INFO @ Sat, 11 Dec 2021 16:53:15: start X-correlation... INFO @ Sat, 11 Dec 2021 16:53:15: end of X-cor INFO @ Sat, 11 Dec 2021 16:53:15: #2 finished! INFO @ Sat, 11 Dec 2021 16:53:15: #2 predicted fragment length is 54 bps INFO @ Sat, 11 Dec 2021 16:53:15: #2 alternative fragment length(s) may be 3,54 bps INFO @ Sat, 11 Dec 2021 16:53:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.20_model.r WARNING @ Sat, 11 Dec 2021 16:53:15: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 16:53:15: #2 You may need to consider one of the other alternative d(s): 3,54 WARNING @ Sat, 11 Dec 2021 16:53:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 16:53:15: #3 Call peaks... INFO @ Sat, 11 Dec 2021 16:53:15: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 16:53:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 16:53:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.20_peaks.xls INFO @ Sat, 11 Dec 2021 16:53:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 16:53:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9427699/SRX9427699.20_summits.bed INFO @ Sat, 11 Dec 2021 16:53:41: Done! pass1 - making usageList (554 chroms): 2 millis pass2 - checking and writing primary data (1473 records, 4 fields): 36 millis CompletedMACS2peakCalling