Job ID = 14172918 SRX = SRX10661194 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: 00:05:54 24742166 reads; of these: 24742166 (100.00%) were unpaired; of these: 1152291 (4.66%) aligned 0 times 14771602 (59.70%) aligned exactly 1 time 8818273 (35.64%) aligned >1 times 95.34% overall alignment rate Time searching: 00:05:54 Overall time: 00:05:54 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] 6406468 / 23589875 = 0.2716 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 17:32:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.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 17:32:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 17:32:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 17:32:27: 1000000 INFO @ Sat, 11 Dec 2021 17:32:33: 2000000 INFO @ Sat, 11 Dec 2021 17:32:38: 3000000 INFO @ Sat, 11 Dec 2021 17:32:43: 4000000 INFO @ Sat, 11 Dec 2021 17:32:48: 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 @ Sat, 11 Dec 2021 17:32:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.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 17:32:52: #1 read tag files... INFO @ Sat, 11 Dec 2021 17:32:52: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 17:32:54: 6000000 INFO @ Sat, 11 Dec 2021 17:32:58: 1000000 INFO @ Sat, 11 Dec 2021 17:32:59: 7000000 INFO @ Sat, 11 Dec 2021 17:33:04: 2000000 INFO @ Sat, 11 Dec 2021 17:33:04: 8000000 INFO @ Sat, 11 Dec 2021 17:33:10: 3000000 INFO @ Sat, 11 Dec 2021 17:33:10: 9000000 INFO @ Sat, 11 Dec 2021 17:33:15: 10000000 INFO @ Sat, 11 Dec 2021 17:33:16: 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 @ Sat, 11 Dec 2021 17:33:21: 11000000 INFO @ Sat, 11 Dec 2021 17:33:21: 5000000 INFO @ Sat, 11 Dec 2021 17:33:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.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 17:33:22: #1 read tag files... INFO @ Sat, 11 Dec 2021 17:33:22: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 17:33:26: 12000000 INFO @ Sat, 11 Dec 2021 17:33:27: 6000000 INFO @ Sat, 11 Dec 2021 17:33:28: 1000000 INFO @ Sat, 11 Dec 2021 17:33:31: 13000000 INFO @ Sat, 11 Dec 2021 17:33:33: 7000000 INFO @ Sat, 11 Dec 2021 17:33:34: 2000000 INFO @ Sat, 11 Dec 2021 17:33:37: 14000000 INFO @ Sat, 11 Dec 2021 17:33:39: 8000000 INFO @ Sat, 11 Dec 2021 17:33:40: 3000000 INFO @ Sat, 11 Dec 2021 17:33:43: 15000000 INFO @ Sat, 11 Dec 2021 17:33:45: 9000000 INFO @ Sat, 11 Dec 2021 17:33:46: 4000000 INFO @ Sat, 11 Dec 2021 17:33:48: 16000000 INFO @ Sat, 11 Dec 2021 17:33:50: 10000000 INFO @ Sat, 11 Dec 2021 17:33:52: 5000000 INFO @ Sat, 11 Dec 2021 17:33:54: 17000000 INFO @ Sat, 11 Dec 2021 17:33:55: #1 tag size is determined as 36 bps INFO @ Sat, 11 Dec 2021 17:33:55: #1 tag size = 36 INFO @ Sat, 11 Dec 2021 17:33:55: #1 total tags in treatment: 17183407 INFO @ Sat, 11 Dec 2021 17:33:55: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 17:33:55: #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 17:33:56: #1 tags after filtering in treatment: 17183353 INFO @ Sat, 11 Dec 2021 17:33:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 17:33:56: #1 finished! INFO @ Sat, 11 Dec 2021 17:33:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 17:33:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 17:33:56: 11000000 INFO @ Sat, 11 Dec 2021 17:33:57: #2 number of paired peaks: 963 WARNING @ Sat, 11 Dec 2021 17:33:57: Fewer paired peaks (963) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 963 pairs to build model! INFO @ Sat, 11 Dec 2021 17:33:57: start model_add_line... INFO @ Sat, 11 Dec 2021 17:33:57: start X-correlation... INFO @ Sat, 11 Dec 2021 17:33:57: end of X-cor INFO @ Sat, 11 Dec 2021 17:33:57: #2 finished! INFO @ Sat, 11 Dec 2021 17:33:57: #2 predicted fragment length is 41 bps INFO @ Sat, 11 Dec 2021 17:33:57: #2 alternative fragment length(s) may be 2,41,564 bps INFO @ Sat, 11 Dec 2021 17:33:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.05_model.r INFO @ Sat, 11 Dec 2021 17:33:58: 6000000 WARNING @ Sat, 11 Dec 2021 17:33:58: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 17:33:58: #2 You may need to consider one of the other alternative d(s): 2,41,564 WARNING @ Sat, 11 Dec 2021 17:33:58: #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 17:33:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 17:33:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 17:34:02: 12000000 INFO @ Sat, 11 Dec 2021 17:34:03: 7000000 INFO @ Sat, 11 Dec 2021 17:34:08: 13000000 INFO @ Sat, 11 Dec 2021 17:34:09: 8000000 INFO @ Sat, 11 Dec 2021 17:34:13: 14000000 INFO @ Sat, 11 Dec 2021 17:34:15: 9000000 INFO @ Sat, 11 Dec 2021 17:34:19: 15000000 INFO @ Sat, 11 Dec 2021 17:34:21: 10000000 INFO @ Sat, 11 Dec 2021 17:34:25: 16000000 INFO @ Sat, 11 Dec 2021 17:34:27: 11000000 INFO @ Sat, 11 Dec 2021 17:34:31: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 17:34:31: 17000000 INFO @ Sat, 11 Dec 2021 17:34:32: #1 tag size is determined as 36 bps INFO @ Sat, 11 Dec 2021 17:34:32: #1 tag size = 36 INFO @ Sat, 11 Dec 2021 17:34:32: #1 total tags in treatment: 17183407 INFO @ Sat, 11 Dec 2021 17:34:32: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 17:34:32: #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 17:34:32: 12000000 INFO @ Sat, 11 Dec 2021 17:34:33: #1 tags after filtering in treatment: 17183353 INFO @ Sat, 11 Dec 2021 17:34:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 17:34:33: #1 finished! INFO @ Sat, 11 Dec 2021 17:34:33: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 17:34:33: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 17:34:34: #2 number of paired peaks: 963 WARNING @ Sat, 11 Dec 2021 17:34:34: Fewer paired peaks (963) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 963 pairs to build model! INFO @ Sat, 11 Dec 2021 17:34:34: start model_add_line... INFO @ Sat, 11 Dec 2021 17:34:34: start X-correlation... INFO @ Sat, 11 Dec 2021 17:34:34: end of X-cor INFO @ Sat, 11 Dec 2021 17:34:34: #2 finished! INFO @ Sat, 11 Dec 2021 17:34:34: #2 predicted fragment length is 41 bps INFO @ Sat, 11 Dec 2021 17:34:34: #2 alternative fragment length(s) may be 2,41,564 bps INFO @ Sat, 11 Dec 2021 17:34:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.10_model.r WARNING @ Sat, 11 Dec 2021 17:34:37: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 17:34:37: #2 You may need to consider one of the other alternative d(s): 2,41,564 WARNING @ Sat, 11 Dec 2021 17:34:37: #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 17:34:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 17:34:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 17:34:38: 13000000 INFO @ Sat, 11 Dec 2021 17:34:43: 14000000 INFO @ Sat, 11 Dec 2021 17:34:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.05_peaks.xls INFO @ Sat, 11 Dec 2021 17:34:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 17:34:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.05_summits.bed INFO @ Sat, 11 Dec 2021 17:34:49: Done! INFO @ Sat, 11 Dec 2021 17:34:49: 15000000 pass1 - making usageList (683 chroms): 2 millis pass2 - checking and writing primary data (7712 records, 4 fields): 100 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 17:34:55: 16000000 INFO @ Sat, 11 Dec 2021 17:35:00: 17000000 INFO @ Sat, 11 Dec 2021 17:35:01: #1 tag size is determined as 36 bps INFO @ Sat, 11 Dec 2021 17:35:01: #1 tag size = 36 INFO @ Sat, 11 Dec 2021 17:35:01: #1 total tags in treatment: 17183407 INFO @ Sat, 11 Dec 2021 17:35:01: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 17:35:01: #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 17:35:02: #1 tags after filtering in treatment: 17183353 INFO @ Sat, 11 Dec 2021 17:35:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 17:35:02: #1 finished! INFO @ Sat, 11 Dec 2021 17:35:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 17:35:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 17:35:03: #2 number of paired peaks: 963 WARNING @ Sat, 11 Dec 2021 17:35:03: Fewer paired peaks (963) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 963 pairs to build model! INFO @ Sat, 11 Dec 2021 17:35:03: start model_add_line... INFO @ Sat, 11 Dec 2021 17:35:03: start X-correlation... INFO @ Sat, 11 Dec 2021 17:35:03: end of X-cor INFO @ Sat, 11 Dec 2021 17:35:03: #2 finished! INFO @ Sat, 11 Dec 2021 17:35:03: #2 predicted fragment length is 41 bps INFO @ Sat, 11 Dec 2021 17:35:03: #2 alternative fragment length(s) may be 2,41,564 bps INFO @ Sat, 11 Dec 2021 17:35:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.20_model.r WARNING @ Sat, 11 Dec 2021 17:35:03: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 17:35:03: #2 You may need to consider one of the other alternative d(s): 2,41,564 WARNING @ Sat, 11 Dec 2021 17:35:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 17:35:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 17:35:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 17:35:08: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 17:35:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.10_peaks.xls INFO @ Sat, 11 Dec 2021 17:35:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 17:35:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.10_summits.bed INFO @ Sat, 11 Dec 2021 17:35:23: Done! pass1 - making usageList (518 chroms): 1 millis pass2 - checking and writing primary data (2915 records, 4 fields): 78 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 17:35:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 17:35:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.20_peaks.xls INFO @ Sat, 11 Dec 2021 17:35:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 17:35:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10661194/SRX10661194.20_summits.bed INFO @ Sat, 11 Dec 2021 17:35:50: Done! pass1 - making usageList (158 chroms): 1 millis pass2 - checking and writing primary data (555 records, 4 fields): 59 millis CompletedMACS2peakCalling