Job ID = 16439013 SRX = SRX10031696 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: 00:11:52 35615026 reads; of these: 35615026 (100.00%) were unpaired; of these: 1023227 (2.87%) aligned 0 times 28259201 (79.35%) aligned exactly 1 time 6332598 (17.78%) aligned >1 times 97.13% overall alignment rate Time searching: 00:11:52 Overall time: 00:11:52 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 16 files... [bam_rmdupse_core] 6691985 / 34591799 = 0.1935 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:45:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.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 @ Tue, 02 Aug 2022 14:45:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:45:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:45:28: 1000000 INFO @ Tue, 02 Aug 2022 14:45:34: 2000000 INFO @ Tue, 02 Aug 2022 14:45:40: 3000000 INFO @ Tue, 02 Aug 2022 14:45:47: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:45:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.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 @ Tue, 02 Aug 2022 14:45:51: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:45:51: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:45:54: 5000000 INFO @ Tue, 02 Aug 2022 14:45:58: 1000000 INFO @ Tue, 02 Aug 2022 14:46:01: 6000000 INFO @ Tue, 02 Aug 2022 14:46:06: 2000000 INFO @ Tue, 02 Aug 2022 14:46:09: 7000000 INFO @ Tue, 02 Aug 2022 14:46:14: 3000000 INFO @ Tue, 02 Aug 2022 14:46:17: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:46:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.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 @ Tue, 02 Aug 2022 14:46:21: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:46:21: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:46:21: 4000000 INFO @ Tue, 02 Aug 2022 14:46:24: 9000000 INFO @ Tue, 02 Aug 2022 14:46:28: 1000000 INFO @ Tue, 02 Aug 2022 14:46:29: 5000000 INFO @ Tue, 02 Aug 2022 14:46:32: 10000000 INFO @ Tue, 02 Aug 2022 14:46:36: 2000000 INFO @ Tue, 02 Aug 2022 14:46:37: 6000000 INFO @ Tue, 02 Aug 2022 14:46:39: 11000000 INFO @ Tue, 02 Aug 2022 14:46:44: 3000000 INFO @ Tue, 02 Aug 2022 14:46:44: 7000000 INFO @ Tue, 02 Aug 2022 14:46:47: 12000000 INFO @ Tue, 02 Aug 2022 14:46:51: 4000000 INFO @ Tue, 02 Aug 2022 14:46:52: 8000000 INFO @ Tue, 02 Aug 2022 14:46:55: 13000000 INFO @ Tue, 02 Aug 2022 14:46:59: 5000000 INFO @ Tue, 02 Aug 2022 14:47:00: 9000000 INFO @ Tue, 02 Aug 2022 14:47:02: 14000000 INFO @ Tue, 02 Aug 2022 14:47:07: 6000000 INFO @ Tue, 02 Aug 2022 14:47:07: 10000000 INFO @ Tue, 02 Aug 2022 14:47:10: 15000000 INFO @ Tue, 02 Aug 2022 14:47:15: 7000000 INFO @ Tue, 02 Aug 2022 14:47:15: 11000000 INFO @ Tue, 02 Aug 2022 14:47:17: 16000000 INFO @ Tue, 02 Aug 2022 14:47:22: 8000000 INFO @ Tue, 02 Aug 2022 14:47:22: 12000000 INFO @ Tue, 02 Aug 2022 14:47:25: 17000000 INFO @ Tue, 02 Aug 2022 14:47:30: 9000000 INFO @ Tue, 02 Aug 2022 14:47:30: 13000000 INFO @ Tue, 02 Aug 2022 14:47:33: 18000000 INFO @ Tue, 02 Aug 2022 14:47:38: 10000000 INFO @ Tue, 02 Aug 2022 14:47:38: 14000000 INFO @ Tue, 02 Aug 2022 14:47:40: 19000000 INFO @ Tue, 02 Aug 2022 14:47:45: 11000000 INFO @ Tue, 02 Aug 2022 14:47:45: 15000000 INFO @ Tue, 02 Aug 2022 14:47:48: 20000000 INFO @ Tue, 02 Aug 2022 14:47:53: 12000000 INFO @ Tue, 02 Aug 2022 14:47:53: 16000000 INFO @ Tue, 02 Aug 2022 14:47:55: 21000000 INFO @ Tue, 02 Aug 2022 14:48:01: 13000000 INFO @ Tue, 02 Aug 2022 14:48:01: 17000000 INFO @ Tue, 02 Aug 2022 14:48:03: 22000000 INFO @ Tue, 02 Aug 2022 14:48:08: 18000000 INFO @ Tue, 02 Aug 2022 14:48:09: 14000000 INFO @ Tue, 02 Aug 2022 14:48:11: 23000000 INFO @ Tue, 02 Aug 2022 14:48:16: 19000000 INFO @ Tue, 02 Aug 2022 14:48:16: 15000000 INFO @ Tue, 02 Aug 2022 14:48:19: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:48:24: 20000000 INFO @ Tue, 02 Aug 2022 14:48:25: 16000000 INFO @ Tue, 02 Aug 2022 14:48:26: 25000000 INFO @ Tue, 02 Aug 2022 14:48:32: 21000000 INFO @ Tue, 02 Aug 2022 14:48:32: 17000000 INFO @ Tue, 02 Aug 2022 14:48:34: 26000000 INFO @ Tue, 02 Aug 2022 14:48:40: 22000000 INFO @ Tue, 02 Aug 2022 14:48:40: 18000000 INFO @ Tue, 02 Aug 2022 14:48:42: 27000000 INFO @ Tue, 02 Aug 2022 14:48:48: 23000000 INFO @ Tue, 02 Aug 2022 14:48:48: 19000000 INFO @ Tue, 02 Aug 2022 14:48:49: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:48:49: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:48:49: #1 total tags in treatment: 27899814 INFO @ Tue, 02 Aug 2022 14:48:49: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:48:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:48:49: #1 tags after filtering in treatment: 27899724 INFO @ Tue, 02 Aug 2022 14:48:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:48:49: #1 finished! INFO @ Tue, 02 Aug 2022 14:48:49: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:48:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:48:51: #2 number of paired peaks: 213 WARNING @ Tue, 02 Aug 2022 14:48:51: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Tue, 02 Aug 2022 14:48:51: start model_add_line... INFO @ Tue, 02 Aug 2022 14:48:51: start X-correlation... INFO @ Tue, 02 Aug 2022 14:48:51: end of X-cor INFO @ Tue, 02 Aug 2022 14:48:51: #2 finished! INFO @ Tue, 02 Aug 2022 14:48:51: #2 predicted fragment length is 69 bps INFO @ Tue, 02 Aug 2022 14:48:51: #2 alternative fragment length(s) may be 1,40,69 bps INFO @ Tue, 02 Aug 2022 14:48:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.05_model.r WARNING @ Tue, 02 Aug 2022 14:48:51: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:48:51: #2 You may need to consider one of the other alternative d(s): 1,40,69 WARNING @ Tue, 02 Aug 2022 14:48:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:48:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:48:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:48:55: 24000000 INFO @ Tue, 02 Aug 2022 14:48:55: 20000000 INFO @ Tue, 02 Aug 2022 14:49:03: 21000000 INFO @ Tue, 02 Aug 2022 14:49:03: 25000000 INFO @ Tue, 02 Aug 2022 14:49:10: 22000000 INFO @ Tue, 02 Aug 2022 14:49:11: 26000000 INFO @ Tue, 02 Aug 2022 14:49:18: 27000000 INFO @ Tue, 02 Aug 2022 14:49:18: 23000000 INFO @ Tue, 02 Aug 2022 14:49:25: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:49:25: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:49:25: #1 total tags in treatment: 27899814 INFO @ Tue, 02 Aug 2022 14:49:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:49:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:49:26: #1 tags after filtering in treatment: 27899724 INFO @ Tue, 02 Aug 2022 14:49:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:49:26: #1 finished! INFO @ Tue, 02 Aug 2022 14:49:26: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:49:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:49:26: 24000000 INFO @ Tue, 02 Aug 2022 14:49:27: #2 number of paired peaks: 213 WARNING @ Tue, 02 Aug 2022 14:49:27: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Tue, 02 Aug 2022 14:49:27: start model_add_line... INFO @ Tue, 02 Aug 2022 14:49:28: start X-correlation... INFO @ Tue, 02 Aug 2022 14:49:28: end of X-cor INFO @ Tue, 02 Aug 2022 14:49:28: #2 finished! INFO @ Tue, 02 Aug 2022 14:49:28: #2 predicted fragment length is 69 bps INFO @ Tue, 02 Aug 2022 14:49:28: #2 alternative fragment length(s) may be 1,40,69 bps INFO @ Tue, 02 Aug 2022 14:49:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.10_model.r WARNING @ Tue, 02 Aug 2022 14:49:28: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:49:28: #2 You may need to consider one of the other alternative d(s): 1,40,69 WARNING @ Tue, 02 Aug 2022 14:49:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:49:28: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:49:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:49:32: 25000000 INFO @ Tue, 02 Aug 2022 14:49:36: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:49:38: 26000000 INFO @ Tue, 02 Aug 2022 14:49:45: 27000000 INFO @ Tue, 02 Aug 2022 14:49:51: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:49:51: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:49:51: #1 total tags in treatment: 27899814 INFO @ Tue, 02 Aug 2022 14:49:51: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:49:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:49:51: #1 tags after filtering in treatment: 27899724 INFO @ Tue, 02 Aug 2022 14:49:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:49:51: #1 finished! INFO @ Tue, 02 Aug 2022 14:49:51: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:49:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:49:53: #2 number of paired peaks: 213 WARNING @ Tue, 02 Aug 2022 14:49:53: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Tue, 02 Aug 2022 14:49:53: start model_add_line... INFO @ Tue, 02 Aug 2022 14:49:53: start X-correlation... INFO @ Tue, 02 Aug 2022 14:49:53: end of X-cor INFO @ Tue, 02 Aug 2022 14:49:53: #2 finished! INFO @ Tue, 02 Aug 2022 14:49:53: #2 predicted fragment length is 69 bps INFO @ Tue, 02 Aug 2022 14:49:53: #2 alternative fragment length(s) may be 1,40,69 bps INFO @ Tue, 02 Aug 2022 14:49:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.20_model.r WARNING @ Tue, 02 Aug 2022 14:49:53: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:49:53: #2 You may need to consider one of the other alternative d(s): 1,40,69 WARNING @ Tue, 02 Aug 2022 14:49:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:49:53: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:49:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:49:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:49:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:49:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.05_summits.bed INFO @ Tue, 02 Aug 2022 14:49:57: Done! pass1 - making usageList (495 chroms): 2 millis pass2 - checking and writing primary data (1619 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:50:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:50:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:50:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:50:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.10_summits.bed INFO @ Tue, 02 Aug 2022 14:50:33: Done! pass1 - making usageList (370 chroms): 2 millis pass2 - checking and writing primary data (951 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:50:39: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:51:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:51:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:51:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX10031696/SRX10031696.20_summits.bed INFO @ Tue, 02 Aug 2022 14:51:00: Done! pass1 - making usageList (207 chroms): 1 millis pass2 - checking and writing primary data (421 records, 4 fields): 22 millis CompletedMACS2peakCalling