Job ID = 14169112 SRX = SRX8688994 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: 00:00:01 Multiseed full-index search: 00:05:19 18500378 reads; of these: 18500378 (100.00%) were unpaired; of these: 989938 (5.35%) aligned 0 times 13693999 (74.02%) aligned exactly 1 time 3816441 (20.63%) aligned >1 times 94.65% overall alignment rate Time searching: 00:05:20 Overall time: 00:05:20 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] 1937930 / 17510440 = 0.1107 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 23:56:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.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 23:56:21: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:56:21: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:56:26: 1000000 INFO @ Fri, 10 Dec 2021 23:56:32: 2000000 INFO @ Fri, 10 Dec 2021 23:56:37: 3000000 INFO @ Fri, 10 Dec 2021 23:56:43: 4000000 INFO @ Fri, 10 Dec 2021 23:56:48: 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 23:56:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.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 23:56:51: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:56:51: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:56:54: 6000000 INFO @ Fri, 10 Dec 2021 23:56:57: 1000000 INFO @ Fri, 10 Dec 2021 23:57:00: 7000000 INFO @ Fri, 10 Dec 2021 23:57:03: 2000000 INFO @ Fri, 10 Dec 2021 23:57:07: 8000000 INFO @ Fri, 10 Dec 2021 23:57:09: 3000000 INFO @ Fri, 10 Dec 2021 23:57:13: 9000000 INFO @ Fri, 10 Dec 2021 23:57:16: 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 23:57:20: 10000000 INFO @ Fri, 10 Dec 2021 23:57:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.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 23:57:21: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:57:21: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:57:23: 5000000 INFO @ Fri, 10 Dec 2021 23:57:27: 11000000 INFO @ Fri, 10 Dec 2021 23:57:28: 1000000 INFO @ Fri, 10 Dec 2021 23:57:30: 6000000 INFO @ Fri, 10 Dec 2021 23:57:33: 12000000 INFO @ Fri, 10 Dec 2021 23:57:35: 2000000 INFO @ Fri, 10 Dec 2021 23:57:36: 7000000 INFO @ Fri, 10 Dec 2021 23:57:40: 13000000 INFO @ Fri, 10 Dec 2021 23:57:41: 3000000 INFO @ Fri, 10 Dec 2021 23:57:42: 8000000 INFO @ Fri, 10 Dec 2021 23:57:48: 4000000 INFO @ Fri, 10 Dec 2021 23:57:48: 14000000 INFO @ Fri, 10 Dec 2021 23:57:49: 9000000 INFO @ Fri, 10 Dec 2021 23:57:54: 5000000 INFO @ Fri, 10 Dec 2021 23:57:55: 15000000 INFO @ Fri, 10 Dec 2021 23:57:56: 10000000 INFO @ Fri, 10 Dec 2021 23:57:59: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 23:57:59: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 23:57:59: #1 total tags in treatment: 15572510 INFO @ Fri, 10 Dec 2021 23:57:59: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:57:59: #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 23:58:00: #1 tags after filtering in treatment: 15572508 INFO @ Fri, 10 Dec 2021 23:58:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 23:58:00: #1 finished! INFO @ Fri, 10 Dec 2021 23:58:00: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:58:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:58:01: 6000000 INFO @ Fri, 10 Dec 2021 23:58:01: #2 number of paired peaks: 137 WARNING @ Fri, 10 Dec 2021 23:58:01: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Fri, 10 Dec 2021 23:58:01: start model_add_line... INFO @ Fri, 10 Dec 2021 23:58:01: start X-correlation... INFO @ Fri, 10 Dec 2021 23:58:01: end of X-cor INFO @ Fri, 10 Dec 2021 23:58:01: #2 finished! INFO @ Fri, 10 Dec 2021 23:58:01: #2 predicted fragment length is 54 bps INFO @ Fri, 10 Dec 2021 23:58:01: #2 alternative fragment length(s) may be 54 bps INFO @ Fri, 10 Dec 2021 23:58:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.05_model.r WARNING @ Fri, 10 Dec 2021 23:58:01: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 23:58:01: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Fri, 10 Dec 2021 23:58:01: #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 23:58:01: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:58:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:58:02: 11000000 INFO @ Fri, 10 Dec 2021 23:58:07: 7000000 INFO @ Fri, 10 Dec 2021 23:58:09: 12000000 INFO @ Fri, 10 Dec 2021 23:58:14: 8000000 INFO @ Fri, 10 Dec 2021 23:58:15: 13000000 INFO @ Fri, 10 Dec 2021 23:58:20: 9000000 INFO @ Fri, 10 Dec 2021 23:58:22: 14000000 INFO @ Fri, 10 Dec 2021 23:58:27: 10000000 INFO @ Fri, 10 Dec 2021 23:58:30: 15000000 INFO @ Fri, 10 Dec 2021 23:58:30: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:58:33: 11000000 INFO @ Fri, 10 Dec 2021 23:58:34: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 23:58:34: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 23:58:34: #1 total tags in treatment: 15572510 INFO @ Fri, 10 Dec 2021 23:58:34: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:58:34: #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 23:58:35: #1 tags after filtering in treatment: 15572508 INFO @ Fri, 10 Dec 2021 23:58:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 23:58:35: #1 finished! INFO @ Fri, 10 Dec 2021 23:58:35: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:58:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:58:36: #2 number of paired peaks: 137 WARNING @ Fri, 10 Dec 2021 23:58:36: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Fri, 10 Dec 2021 23:58:36: start model_add_line... INFO @ Fri, 10 Dec 2021 23:58:36: start X-correlation... INFO @ Fri, 10 Dec 2021 23:58:36: end of X-cor INFO @ Fri, 10 Dec 2021 23:58:36: #2 finished! INFO @ Fri, 10 Dec 2021 23:58:36: #2 predicted fragment length is 54 bps INFO @ Fri, 10 Dec 2021 23:58:36: #2 alternative fragment length(s) may be 54 bps INFO @ Fri, 10 Dec 2021 23:58:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.10_model.r WARNING @ Fri, 10 Dec 2021 23:58:36: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 23:58:36: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Fri, 10 Dec 2021 23:58:36: #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 23:58:36: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:58:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:58:39: 12000000 INFO @ Fri, 10 Dec 2021 23:58:45: 13000000 INFO @ Fri, 10 Dec 2021 23:58:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.05_peaks.xls INFO @ Fri, 10 Dec 2021 23:58:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:58:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.05_summits.bed INFO @ Fri, 10 Dec 2021 23:58:48: Done! pass1 - making usageList (420 chroms): 1 millis pass2 - checking and writing primary data (2066 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 23:58:52: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 23:58:58: 15000000 INFO @ Fri, 10 Dec 2021 23:59:02: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 23:59:02: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 23:59:02: #1 total tags in treatment: 15572510 INFO @ Fri, 10 Dec 2021 23:59:02: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:59:02: #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 23:59:03: #1 tags after filtering in treatment: 15572508 INFO @ Fri, 10 Dec 2021 23:59:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 23:59:03: #1 finished! INFO @ Fri, 10 Dec 2021 23:59:03: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:59:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:59:04: #2 number of paired peaks: 137 WARNING @ Fri, 10 Dec 2021 23:59:04: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Fri, 10 Dec 2021 23:59:04: start model_add_line... INFO @ Fri, 10 Dec 2021 23:59:04: start X-correlation... INFO @ Fri, 10 Dec 2021 23:59:04: end of X-cor INFO @ Fri, 10 Dec 2021 23:59:04: #2 finished! INFO @ Fri, 10 Dec 2021 23:59:04: #2 predicted fragment length is 54 bps INFO @ Fri, 10 Dec 2021 23:59:04: #2 alternative fragment length(s) may be 54 bps INFO @ Fri, 10 Dec 2021 23:59:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.20_model.r WARNING @ Fri, 10 Dec 2021 23:59:04: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 23:59:04: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Fri, 10 Dec 2021 23:59:04: #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 23:59:04: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:59:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:59:05: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:59:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.10_peaks.xls INFO @ Fri, 10 Dec 2021 23:59:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:59:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.10_summits.bed INFO @ Fri, 10 Dec 2021 23:59:22: Done! pass1 - making usageList (285 chroms): 1 millis pass2 - checking and writing primary data (743 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 23:59:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 23:59:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.20_peaks.xls INFO @ Fri, 10 Dec 2021 23:59:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:59:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688994/SRX8688994.20_summits.bed INFO @ Fri, 10 Dec 2021 23:59:50: Done! pass1 - making usageList (112 chroms): 1 millis pass2 - checking and writing primary data (215 records, 4 fields): 402 millis CompletedMACS2peakCalling