Job ID = 16439999 SRX = SRX8369898 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: 00:09:20 42790523 reads; of these: 42790523 (100.00%) were unpaired; of these: 6799092 (15.89%) aligned 0 times 28254756 (66.03%) aligned exactly 1 time 7736675 (18.08%) aligned >1 times 84.11% overall alignment rate Time searching: 00:09:20 Overall time: 00:09:20 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 16 files... [bam_rmdupse_core] 7798319 / 35991431 = 0.2167 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 16:49:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.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 16:49:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:49:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:50:03: 1000000 INFO @ Tue, 02 Aug 2022 16:50:09: 2000000 INFO @ Tue, 02 Aug 2022 16:50:15: 3000000 INFO @ Tue, 02 Aug 2022 16:50:21: 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 16:50:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.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 16:50:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:50:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:50:27: 5000000 INFO @ Tue, 02 Aug 2022 16:50:33: 1000000 INFO @ Tue, 02 Aug 2022 16:50:34: 6000000 INFO @ Tue, 02 Aug 2022 16:50:39: 2000000 INFO @ Tue, 02 Aug 2022 16:50:41: 7000000 INFO @ Tue, 02 Aug 2022 16:50:45: 3000000 INFO @ Tue, 02 Aug 2022 16:50:48: 8000000 INFO @ Tue, 02 Aug 2022 16:50:52: 4000000 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 16:50:55: 9000000 INFO @ Tue, 02 Aug 2022 16:50:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.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 16:50:56: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:50:56: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:50:58: 5000000 INFO @ Tue, 02 Aug 2022 16:51:02: 10000000 INFO @ Tue, 02 Aug 2022 16:51:03: 1000000 INFO @ Tue, 02 Aug 2022 16:51:04: 6000000 INFO @ Tue, 02 Aug 2022 16:51:09: 11000000 INFO @ Tue, 02 Aug 2022 16:51:10: 2000000 INFO @ Tue, 02 Aug 2022 16:51:11: 7000000 INFO @ Tue, 02 Aug 2022 16:51:16: 12000000 INFO @ Tue, 02 Aug 2022 16:51:17: 3000000 INFO @ Tue, 02 Aug 2022 16:51:17: 8000000 INFO @ Tue, 02 Aug 2022 16:51:23: 13000000 INFO @ Tue, 02 Aug 2022 16:51:24: 4000000 INFO @ Tue, 02 Aug 2022 16:51:24: 9000000 INFO @ Tue, 02 Aug 2022 16:51:29: 14000000 INFO @ Tue, 02 Aug 2022 16:51:30: 10000000 INFO @ Tue, 02 Aug 2022 16:51:30: 5000000 INFO @ Tue, 02 Aug 2022 16:51:36: 15000000 INFO @ Tue, 02 Aug 2022 16:51:37: 11000000 INFO @ Tue, 02 Aug 2022 16:51:37: 6000000 INFO @ Tue, 02 Aug 2022 16:51:43: 16000000 INFO @ Tue, 02 Aug 2022 16:51:43: 12000000 INFO @ Tue, 02 Aug 2022 16:51:45: 7000000 INFO @ Tue, 02 Aug 2022 16:51:50: 13000000 INFO @ Tue, 02 Aug 2022 16:51:50: 17000000 INFO @ Tue, 02 Aug 2022 16:51:51: 8000000 INFO @ Tue, 02 Aug 2022 16:51:56: 14000000 INFO @ Tue, 02 Aug 2022 16:51:57: 18000000 INFO @ Tue, 02 Aug 2022 16:51:58: 9000000 INFO @ Tue, 02 Aug 2022 16:52:03: 15000000 INFO @ Tue, 02 Aug 2022 16:52:03: 19000000 INFO @ Tue, 02 Aug 2022 16:52:05: 10000000 INFO @ Tue, 02 Aug 2022 16:52:09: 16000000 INFO @ Tue, 02 Aug 2022 16:52:10: 20000000 INFO @ Tue, 02 Aug 2022 16:52:12: 11000000 INFO @ Tue, 02 Aug 2022 16:52:16: 17000000 INFO @ Tue, 02 Aug 2022 16:52:17: 21000000 INFO @ Tue, 02 Aug 2022 16:52:19: 12000000 INFO @ Tue, 02 Aug 2022 16:52:22: 18000000 INFO @ Tue, 02 Aug 2022 16:52:24: 22000000 INFO @ Tue, 02 Aug 2022 16:52:25: 13000000 INFO @ Tue, 02 Aug 2022 16:52:29: 19000000 INFO @ Tue, 02 Aug 2022 16:52:31: 23000000 INFO @ Tue, 02 Aug 2022 16:52:32: 14000000 INFO @ Tue, 02 Aug 2022 16:52:35: 20000000 INFO @ Tue, 02 Aug 2022 16:52:37: 24000000 INFO @ Tue, 02 Aug 2022 16:52:39: 15000000 INFO @ Tue, 02 Aug 2022 16:52:42: 21000000 INFO @ Tue, 02 Aug 2022 16:52:44: 25000000 INFO @ Tue, 02 Aug 2022 16:52:46: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:52:48: 22000000 INFO @ Tue, 02 Aug 2022 16:52:51: 26000000 INFO @ Tue, 02 Aug 2022 16:52:53: 17000000 INFO @ Tue, 02 Aug 2022 16:52:55: 23000000 INFO @ Tue, 02 Aug 2022 16:52:57: 27000000 INFO @ Tue, 02 Aug 2022 16:52:59: 18000000 INFO @ Tue, 02 Aug 2022 16:53:02: 24000000 INFO @ Tue, 02 Aug 2022 16:53:04: 28000000 INFO @ Tue, 02 Aug 2022 16:53:06: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 16:53:06: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 16:53:06: #1 total tags in treatment: 28193112 INFO @ Tue, 02 Aug 2022 16:53:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:53:06: #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 16:53:06: 19000000 INFO @ Tue, 02 Aug 2022 16:53:06: #1 tags after filtering in treatment: 28193112 INFO @ Tue, 02 Aug 2022 16:53:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:53:06: #1 finished! INFO @ Tue, 02 Aug 2022 16:53:06: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:53:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:53:08: 25000000 INFO @ Tue, 02 Aug 2022 16:53:08: #2 number of paired peaks: 193 WARNING @ Tue, 02 Aug 2022 16:53:08: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Tue, 02 Aug 2022 16:53:08: start model_add_line... INFO @ Tue, 02 Aug 2022 16:53:08: start X-correlation... INFO @ Tue, 02 Aug 2022 16:53:09: end of X-cor INFO @ Tue, 02 Aug 2022 16:53:09: #2 finished! INFO @ Tue, 02 Aug 2022 16:53:09: #2 predicted fragment length is 49 bps INFO @ Tue, 02 Aug 2022 16:53:09: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 02 Aug 2022 16:53:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.05_model.r WARNING @ Tue, 02 Aug 2022 16:53:09: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:53:09: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 02 Aug 2022 16:53:09: #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 16:53:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:53:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:53:13: 20000000 INFO @ Tue, 02 Aug 2022 16:53:14: 26000000 INFO @ Tue, 02 Aug 2022 16:53:19: 21000000 INFO @ Tue, 02 Aug 2022 16:53:21: 27000000 INFO @ Tue, 02 Aug 2022 16:53:26: 22000000 INFO @ Tue, 02 Aug 2022 16:53:27: 28000000 INFO @ Tue, 02 Aug 2022 16:53:29: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 16:53:29: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 16:53:29: #1 total tags in treatment: 28193112 INFO @ Tue, 02 Aug 2022 16:53:29: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:53:29: #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 16:53:29: #1 tags after filtering in treatment: 28193112 INFO @ Tue, 02 Aug 2022 16:53:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:53:29: #1 finished! INFO @ Tue, 02 Aug 2022 16:53:29: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:53:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:53:31: #2 number of paired peaks: 193 WARNING @ Tue, 02 Aug 2022 16:53:31: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Tue, 02 Aug 2022 16:53:31: start model_add_line... INFO @ Tue, 02 Aug 2022 16:53:31: start X-correlation... INFO @ Tue, 02 Aug 2022 16:53:31: end of X-cor INFO @ Tue, 02 Aug 2022 16:53:31: #2 finished! INFO @ Tue, 02 Aug 2022 16:53:31: #2 predicted fragment length is 49 bps INFO @ Tue, 02 Aug 2022 16:53:31: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 02 Aug 2022 16:53:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.10_model.r WARNING @ Tue, 02 Aug 2022 16:53:32: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:53:32: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 02 Aug 2022 16:53:32: #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 16:53:32: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:53:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:53:33: 23000000 INFO @ Tue, 02 Aug 2022 16:53:39: 24000000 INFO @ Tue, 02 Aug 2022 16:53:45: 25000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:53:51: 26000000 INFO @ Tue, 02 Aug 2022 16:53:51: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:53:57: 27000000 INFO @ Tue, 02 Aug 2022 16:54:03: 28000000 INFO @ Tue, 02 Aug 2022 16:54:04: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 16:54:04: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 16:54:04: #1 total tags in treatment: 28193112 INFO @ Tue, 02 Aug 2022 16:54:04: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:54:04: #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 16:54:05: #1 tags after filtering in treatment: 28193112 INFO @ Tue, 02 Aug 2022 16:54:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:54:05: #1 finished! INFO @ Tue, 02 Aug 2022 16:54:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:54:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:54:07: #2 number of paired peaks: 193 WARNING @ Tue, 02 Aug 2022 16:54:07: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Tue, 02 Aug 2022 16:54:07: start model_add_line... INFO @ Tue, 02 Aug 2022 16:54:07: start X-correlation... INFO @ Tue, 02 Aug 2022 16:54:07: end of X-cor INFO @ Tue, 02 Aug 2022 16:54:07: #2 finished! INFO @ Tue, 02 Aug 2022 16:54:07: #2 predicted fragment length is 49 bps INFO @ Tue, 02 Aug 2022 16:54:07: #2 alternative fragment length(s) may be 3,49 bps INFO @ Tue, 02 Aug 2022 16:54:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.20_model.r WARNING @ Tue, 02 Aug 2022 16:54:07: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:54:07: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Tue, 02 Aug 2022 16:54:07: #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 16:54:07: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:54:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:54:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:54:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:54:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.05_summits.bed INFO @ Tue, 02 Aug 2022 16:54:13: Done! pass1 - making usageList (677 chroms): 3 millis pass2 - checking and writing primary data (9150 records, 4 fields): 48 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:54:17: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:54:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:54:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:54:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.10_summits.bed INFO @ Tue, 02 Aug 2022 16:54:40: Done! pass1 - making usageList (488 chroms): 1 millis pass2 - checking and writing primary data (4990 records, 4 fields): 64 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:54:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:55:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:55:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:55:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8369898/SRX8369898.20_summits.bed INFO @ Tue, 02 Aug 2022 16:55:16: Done! pass1 - making usageList (307 chroms): 1 millis pass2 - checking and writing primary data (1718 records, 4 fields): 54 millis CompletedMACS2peakCalling