Job ID = 16438596 SRX = SRX10031696 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 35615026 spots for SRR13634466/SRR13634466.sra Written 35615026 spots for SRR13634466/SRR13634466.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439013 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:18:08 35615026 reads; of these: 35615026 (100.00%) were unpaired; of these: 932908 (2.62%) aligned 0 times 27291963 (76.63%) aligned exactly 1 time 7390155 (20.75%) aligned >1 times 97.38% overall alignment rate Time searching: 00:18:08 Overall time: 00:18:08 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 5924505 / 34682118 = 0.1708 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 14:34:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031696/SRX10031696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031696/SRX10031696.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031696/SRX10031696.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/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 14:34:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:34:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:34:26: 1000000 INFO @ Tue, 02 Aug 2022 14:34:37: 2000000 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 14:34:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031696/SRX10031696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031696/SRX10031696.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031696/SRX10031696.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/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 14:34:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:34:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:34:49: 3000000 INFO @ Tue, 02 Aug 2022 14:34:57: 1000000 INFO @ Tue, 02 Aug 2022 14:34:59: 4000000 INFO @ Tue, 02 Aug 2022 14:35:08: 2000000 INFO @ Tue, 02 Aug 2022 14:35:10: 5000000 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 14:35:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031696/SRX10031696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031696/SRX10031696.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031696/SRX10031696.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/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 14:35:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:35:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:35:19: 3000000 INFO @ Tue, 02 Aug 2022 14:35:21: 6000000 INFO @ Tue, 02 Aug 2022 14:35:26: 1000000 INFO @ Tue, 02 Aug 2022 14:35:31: 4000000 INFO @ Tue, 02 Aug 2022 14:35:32: 7000000 INFO @ Tue, 02 Aug 2022 14:35:36: 2000000 INFO @ Tue, 02 Aug 2022 14:35:43: 8000000 INFO @ Tue, 02 Aug 2022 14:35:43: 5000000 INFO @ Tue, 02 Aug 2022 14:35:46: 3000000 INFO @ Tue, 02 Aug 2022 14:35:54: 9000000 INFO @ Tue, 02 Aug 2022 14:35:56: 6000000 INFO @ Tue, 02 Aug 2022 14:35:57: 4000000 INFO @ Tue, 02 Aug 2022 14:36:04: 10000000 INFO @ Tue, 02 Aug 2022 14:36:08: 5000000 INFO @ Tue, 02 Aug 2022 14:36:08: 7000000 INFO @ Tue, 02 Aug 2022 14:36:14: 11000000 INFO @ Tue, 02 Aug 2022 14:36:19: 6000000 INFO @ Tue, 02 Aug 2022 14:36:20: 8000000 INFO @ Tue, 02 Aug 2022 14:36:24: 12000000 INFO @ Tue, 02 Aug 2022 14:36:30: 9000000 INFO @ Tue, 02 Aug 2022 14:36:31: 7000000 INFO @ Tue, 02 Aug 2022 14:36:34: 13000000 INFO @ Tue, 02 Aug 2022 14:36:41: 10000000 INFO @ Tue, 02 Aug 2022 14:36:42: 8000000 INFO @ Tue, 02 Aug 2022 14:36:44: 14000000 INFO @ Tue, 02 Aug 2022 14:36:52: 11000000 INFO @ Tue, 02 Aug 2022 14:36:53: 9000000 INFO @ Tue, 02 Aug 2022 14:36:53: 15000000 INFO @ Tue, 02 Aug 2022 14:37:02: 12000000 INFO @ Tue, 02 Aug 2022 14:37:03: 16000000 INFO @ Tue, 02 Aug 2022 14:37:04: 10000000 INFO @ Tue, 02 Aug 2022 14:37:14: 17000000 INFO @ Tue, 02 Aug 2022 14:37:14: 13000000 INFO @ Tue, 02 Aug 2022 14:37:15: 11000000 INFO @ Tue, 02 Aug 2022 14:37:23: 18000000 INFO @ Tue, 02 Aug 2022 14:37:25: 14000000 INFO @ Tue, 02 Aug 2022 14:37:25: 12000000 INFO @ Tue, 02 Aug 2022 14:37:33: 19000000 INFO @ Tue, 02 Aug 2022 14:37:35: 15000000 INFO @ Tue, 02 Aug 2022 14:37:35: 13000000 INFO @ Tue, 02 Aug 2022 14:37:43: 20000000 INFO @ Tue, 02 Aug 2022 14:37:45: 14000000 INFO @ Tue, 02 Aug 2022 14:37:45: 16000000 INFO @ Tue, 02 Aug 2022 14:37:53: 21000000 INFO @ Tue, 02 Aug 2022 14:37:55: 15000000 INFO @ Tue, 02 Aug 2022 14:37:55: 17000000 INFO @ Tue, 02 Aug 2022 14:38:03: 22000000 INFO @ Tue, 02 Aug 2022 14:38:05: 16000000 INFO @ Tue, 02 Aug 2022 14:38:05: 18000000 INFO @ Tue, 02 Aug 2022 14:38:14: 23000000 INFO @ Tue, 02 Aug 2022 14:38:15: 17000000 INFO @ Tue, 02 Aug 2022 14:38:16: 19000000 INFO @ Tue, 02 Aug 2022 14:38:24: 24000000 INFO @ Tue, 02 Aug 2022 14:38:26: 18000000 INFO @ Tue, 02 Aug 2022 14:38:26: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:38:35: 25000000 INFO @ Tue, 02 Aug 2022 14:38:36: 19000000 INFO @ Tue, 02 Aug 2022 14:38:36: 21000000 INFO @ Tue, 02 Aug 2022 14:38:45: 26000000 INFO @ Tue, 02 Aug 2022 14:38:46: 20000000 INFO @ Tue, 02 Aug 2022 14:38:47: 22000000 INFO @ Tue, 02 Aug 2022 14:38:55: 27000000 INFO @ Tue, 02 Aug 2022 14:38:57: 21000000 INFO @ Tue, 02 Aug 2022 14:38:57: 23000000 INFO @ Tue, 02 Aug 2022 14:39:04: 28000000 INFO @ Tue, 02 Aug 2022 14:39:07: 22000000 INFO @ Tue, 02 Aug 2022 14:39:07: 24000000 INFO @ Tue, 02 Aug 2022 14:39:12: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:39:12: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:39:12: #1 total tags in treatment: 28757613 INFO @ Tue, 02 Aug 2022 14:39:12: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:39:12: #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 14:39:12: #1 tags after filtering in treatment: 28757613 INFO @ Tue, 02 Aug 2022 14:39:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:39:12: #1 finished! INFO @ Tue, 02 Aug 2022 14:39:12: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:39:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:39:14: #2 number of paired peaks: 118 WARNING @ Tue, 02 Aug 2022 14:39:14: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Tue, 02 Aug 2022 14:39:14: start model_add_line... INFO @ Tue, 02 Aug 2022 14:39:15: start X-correlation... INFO @ Tue, 02 Aug 2022 14:39:15: end of X-cor INFO @ Tue, 02 Aug 2022 14:39:15: #2 finished! INFO @ Tue, 02 Aug 2022 14:39:15: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 14:39:15: #2 alternative fragment length(s) may be 1,38,75,572 bps INFO @ Tue, 02 Aug 2022 14:39:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031696/SRX10031696.05_model.r WARNING @ Tue, 02 Aug 2022 14:39:15: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:39:15: #2 You may need to consider one of the other alternative d(s): 1,38,75,572 WARNING @ Tue, 02 Aug 2022 14:39:15: #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 14:39:15: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:39:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:39:17: 23000000 INFO @ Tue, 02 Aug 2022 14:39:18: 25000000 INFO @ Tue, 02 Aug 2022 14:39:28: 26000000 INFO @ Tue, 02 Aug 2022 14:39:29: 24000000 INFO @ Tue, 02 Aug 2022 14:39:38: 27000000 INFO @ Tue, 02 Aug 2022 14:39:40: 25000000 INFO @ Tue, 02 Aug 2022 14:39:48: 28000000 INFO @ Tue, 02 Aug 2022 14:39:52: 26000000 INFO @ Tue, 02 Aug 2022 14:39:56: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:39:56: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:39:56: #1 total tags in treatment: 28757613 INFO @ Tue, 02 Aug 2022 14:39:56: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:39:56: #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 14:39:57: #1 tags after filtering in treatment: 28757613 INFO @ Tue, 02 Aug 2022 14:39:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:39:57: #1 finished! INFO @ Tue, 02 Aug 2022 14:39:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:39:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:39:59: #2 number of paired peaks: 118 WARNING @ Tue, 02 Aug 2022 14:39:59: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Tue, 02 Aug 2022 14:39:59: start model_add_line... INFO @ Tue, 02 Aug 2022 14:39:59: start X-correlation... INFO @ Tue, 02 Aug 2022 14:39:59: end of X-cor INFO @ Tue, 02 Aug 2022 14:39:59: #2 finished! INFO @ Tue, 02 Aug 2022 14:39:59: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 14:39:59: #2 alternative fragment length(s) may be 1,38,75,572 bps INFO @ Tue, 02 Aug 2022 14:39:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031696/SRX10031696.10_model.r WARNING @ Tue, 02 Aug 2022 14:39:59: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:39:59: #2 You may need to consider one of the other alternative d(s): 1,38,75,572 WARNING @ Tue, 02 Aug 2022 14:39:59: #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 14:39:59: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:39:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:40:02: 27000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:40:11: 28000000 INFO @ Tue, 02 Aug 2022 14:40:19: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:40:19: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:40:19: #1 total tags in treatment: 28757613 INFO @ Tue, 02 Aug 2022 14:40:19: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:40:19: #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 14:40:19: #1 tags after filtering in treatment: 28757613 INFO @ Tue, 02 Aug 2022 14:40:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:40:19: #1 finished! INFO @ Tue, 02 Aug 2022 14:40:19: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:40:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:40:21: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:40:21: #2 number of paired peaks: 118 WARNING @ Tue, 02 Aug 2022 14:40:21: Fewer paired peaks (118) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 118 pairs to build model! INFO @ Tue, 02 Aug 2022 14:40:21: start model_add_line... INFO @ Tue, 02 Aug 2022 14:40:22: start X-correlation... INFO @ Tue, 02 Aug 2022 14:40:22: end of X-cor INFO @ Tue, 02 Aug 2022 14:40:22: #2 finished! INFO @ Tue, 02 Aug 2022 14:40:22: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 14:40:22: #2 alternative fragment length(s) may be 1,38,75,572 bps INFO @ Tue, 02 Aug 2022 14:40:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031696/SRX10031696.20_model.r WARNING @ Tue, 02 Aug 2022 14:40:22: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:40:22: #2 You may need to consider one of the other alternative d(s): 1,38,75,572 WARNING @ Tue, 02 Aug 2022 14:40:22: #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 14:40:22: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:40:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:40:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031696/SRX10031696.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:40:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031696/SRX10031696.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:40:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031696/SRX10031696.05_summits.bed INFO @ Tue, 02 Aug 2022 14:40:55: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1128 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:41:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:41:27: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:41:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031696/SRX10031696.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:41:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031696/SRX10031696.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:41:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031696/SRX10031696.10_summits.bed INFO @ Tue, 02 Aug 2022 14:41:41: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (658 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:42:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031696/SRX10031696.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:42:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031696/SRX10031696.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:42:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031696/SRX10031696.20_summits.bed INFO @ Tue, 02 Aug 2022 14:42:02: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (330 records, 4 fields): 21 millis CompletedMACS2peakCalling