Job ID = 12265518 SRX = SRX7191479 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: 00:05:26 21282276 reads; of these: 21282276 (100.00%) were unpaired; of these: 3963636 (18.62%) aligned 0 times 15068035 (70.80%) aligned exactly 1 time 2250605 (10.58%) aligned >1 times 81.38% overall alignment rate Time searching: 00:05:26 Overall time: 00:05:26 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] 6277092 / 17318640 = 0.3624 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:33:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.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, 03 Apr 2021 07:33:29: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:33:29: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:33:37: 1000000 INFO @ Sat, 03 Apr 2021 07:33:45: 2000000 INFO @ Sat, 03 Apr 2021 07:33:53: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:33:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.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, 03 Apr 2021 07:33:59: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:33:59: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:34:01: 4000000 INFO @ Sat, 03 Apr 2021 07:34:08: 1000000 INFO @ Sat, 03 Apr 2021 07:34:09: 5000000 INFO @ Sat, 03 Apr 2021 07:34:16: 2000000 INFO @ Sat, 03 Apr 2021 07:34:18: 6000000 INFO @ Sat, 03 Apr 2021 07:34:25: 3000000 INFO @ Sat, 03 Apr 2021 07:34:26: 7000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:34:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.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, 03 Apr 2021 07:34:29: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:34:29: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:34:33: 4000000 INFO @ Sat, 03 Apr 2021 07:34:35: 8000000 INFO @ Sat, 03 Apr 2021 07:34:37: 1000000 INFO @ Sat, 03 Apr 2021 07:34:42: 5000000 INFO @ Sat, 03 Apr 2021 07:34:44: 9000000 INFO @ Sat, 03 Apr 2021 07:34:45: 2000000 INFO @ Sat, 03 Apr 2021 07:34:50: 6000000 INFO @ Sat, 03 Apr 2021 07:34:53: 10000000 INFO @ Sat, 03 Apr 2021 07:34:53: 3000000 INFO @ Sat, 03 Apr 2021 07:34:59: 7000000 INFO @ Sat, 03 Apr 2021 07:35:01: 4000000 INFO @ Sat, 03 Apr 2021 07:35:01: 11000000 INFO @ Sat, 03 Apr 2021 07:35:02: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:35:02: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:35:02: #1 total tags in treatment: 11041548 INFO @ Sat, 03 Apr 2021 07:35:02: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:35:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:35:02: #1 tags after filtering in treatment: 11041405 INFO @ Sat, 03 Apr 2021 07:35:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:35:02: #1 finished! INFO @ Sat, 03 Apr 2021 07:35:02: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:35:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:35:03: #2 number of paired peaks: 359 WARNING @ Sat, 03 Apr 2021 07:35:03: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Sat, 03 Apr 2021 07:35:03: start model_add_line... INFO @ Sat, 03 Apr 2021 07:35:03: start X-correlation... INFO @ Sat, 03 Apr 2021 07:35:03: end of X-cor INFO @ Sat, 03 Apr 2021 07:35:03: #2 finished! INFO @ Sat, 03 Apr 2021 07:35:03: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Apr 2021 07:35:03: #2 alternative fragment length(s) may be 55 bps INFO @ Sat, 03 Apr 2021 07:35:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.05_model.r WARNING @ Sat, 03 Apr 2021 07:35:03: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:35:03: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sat, 03 Apr 2021 07:35:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:35:03: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:35:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:35:07: 8000000 INFO @ Sat, 03 Apr 2021 07:35:09: 5000000 INFO @ Sat, 03 Apr 2021 07:35:16: 9000000 INFO @ Sat, 03 Apr 2021 07:35:17: 6000000 INFO @ Sat, 03 Apr 2021 07:35:24: 10000000 INFO @ Sat, 03 Apr 2021 07:35:25: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:35:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:35:32: 11000000 INFO @ Sat, 03 Apr 2021 07:35:33: 8000000 INFO @ Sat, 03 Apr 2021 07:35:33: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:35:33: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:35:33: #1 total tags in treatment: 11041548 INFO @ Sat, 03 Apr 2021 07:35:33: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:35:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:35:33: #1 tags after filtering in treatment: 11041405 INFO @ Sat, 03 Apr 2021 07:35:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:35:33: #1 finished! INFO @ Sat, 03 Apr 2021 07:35:33: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:35:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:35:34: #2 number of paired peaks: 359 WARNING @ Sat, 03 Apr 2021 07:35:34: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Sat, 03 Apr 2021 07:35:34: start model_add_line... INFO @ Sat, 03 Apr 2021 07:35:34: start X-correlation... INFO @ Sat, 03 Apr 2021 07:35:34: end of X-cor INFO @ Sat, 03 Apr 2021 07:35:34: #2 finished! INFO @ Sat, 03 Apr 2021 07:35:34: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Apr 2021 07:35:34: #2 alternative fragment length(s) may be 55 bps INFO @ Sat, 03 Apr 2021 07:35:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.10_model.r WARNING @ Sat, 03 Apr 2021 07:35:34: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:35:34: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sat, 03 Apr 2021 07:35:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:35:34: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:35:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:35:40: 9000000 INFO @ Sat, 03 Apr 2021 07:35:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:35:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:35:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.05_summits.bed INFO @ Sat, 03 Apr 2021 07:35:43: Done! pass1 - making usageList (162 chroms): 2 millis pass2 - checking and writing primary data (5467 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:35:46: 10000000 INFO @ Sat, 03 Apr 2021 07:35:52: 11000000 INFO @ Sat, 03 Apr 2021 07:35:52: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:35:52: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:35:52: #1 total tags in treatment: 11041548 INFO @ Sat, 03 Apr 2021 07:35:52: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:35:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:35:53: #1 tags after filtering in treatment: 11041405 INFO @ Sat, 03 Apr 2021 07:35:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:35:53: #1 finished! INFO @ Sat, 03 Apr 2021 07:35:53: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:35:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:35:54: #2 number of paired peaks: 359 WARNING @ Sat, 03 Apr 2021 07:35:54: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Sat, 03 Apr 2021 07:35:54: start model_add_line... INFO @ Sat, 03 Apr 2021 07:35:54: start X-correlation... INFO @ Sat, 03 Apr 2021 07:35:54: end of X-cor INFO @ Sat, 03 Apr 2021 07:35:54: #2 finished! INFO @ Sat, 03 Apr 2021 07:35:54: #2 predicted fragment length is 55 bps INFO @ Sat, 03 Apr 2021 07:35:54: #2 alternative fragment length(s) may be 55 bps INFO @ Sat, 03 Apr 2021 07:35:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.20_model.r WARNING @ Sat, 03 Apr 2021 07:35:54: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:35:54: #2 You may need to consider one of the other alternative d(s): 55 WARNING @ Sat, 03 Apr 2021 07:35:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:35:54: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:35:54: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:35:58: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:36:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:36:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:36:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.10_summits.bed INFO @ Sat, 03 Apr 2021 07:36:11: Done! pass1 - making usageList (89 chroms): 1 millis pass2 - checking and writing primary data (1077 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:36:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:36:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:36:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:36:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7191479/SRX7191479.20_summits.bed INFO @ Sat, 03 Apr 2021 07:36:32: Done! pass1 - making usageList (59 chroms): 1 millis pass2 - checking and writing primary data (110 records, 4 fields): 3 millis CompletedMACS2peakCalling