Job ID = 16438594 SRX = SRX10031694 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 39752650 spots for SRR13634464/SRR13634464.sra Written 39752650 spots for SRR13634464/SRR13634464.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439122 ("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: 00:21:05 39752650 reads; of these: 39752650 (100.00%) were unpaired; of these: 1091287 (2.75%) aligned 0 times 30439953 (76.57%) aligned exactly 1 time 8221410 (20.68%) aligned >1 times 97.25% overall alignment rate Time searching: 00:21:05 Overall time: 00:21:05 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] 6532334 / 38661363 = 0.1690 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 14:38:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.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 14:38:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:38:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:38:41: 1000000 INFO @ Tue, 02 Aug 2022 14:38:52: 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 14:38:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.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 14:38:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:38:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:39:03: 3000000 INFO @ Tue, 02 Aug 2022 14:39:08: 1000000 INFO @ Tue, 02 Aug 2022 14:39:13: 4000000 INFO @ Tue, 02 Aug 2022 14:39:19: 2000000 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 14:39:26: 5000000 INFO @ Tue, 02 Aug 2022 14:39:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.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 14:39:27: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:39:27: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:39:31: 3000000 INFO @ Tue, 02 Aug 2022 14:39:38: 6000000 INFO @ Tue, 02 Aug 2022 14:39:40: 1000000 INFO @ Tue, 02 Aug 2022 14:39:44: 4000000 INFO @ Tue, 02 Aug 2022 14:39:51: 7000000 INFO @ Tue, 02 Aug 2022 14:39:54: 2000000 INFO @ Tue, 02 Aug 2022 14:39:57: 5000000 INFO @ Tue, 02 Aug 2022 14:40:04: 8000000 INFO @ Tue, 02 Aug 2022 14:40:08: 3000000 INFO @ Tue, 02 Aug 2022 14:40:09: 6000000 INFO @ Tue, 02 Aug 2022 14:40:17: 9000000 INFO @ Tue, 02 Aug 2022 14:40:21: 4000000 INFO @ Tue, 02 Aug 2022 14:40:21: 7000000 INFO @ Tue, 02 Aug 2022 14:40:29: 10000000 INFO @ Tue, 02 Aug 2022 14:40:34: 8000000 INFO @ Tue, 02 Aug 2022 14:40:34: 5000000 INFO @ Tue, 02 Aug 2022 14:40:41: 11000000 INFO @ Tue, 02 Aug 2022 14:40:45: 9000000 INFO @ Tue, 02 Aug 2022 14:40:47: 6000000 INFO @ Tue, 02 Aug 2022 14:40:53: 12000000 INFO @ Tue, 02 Aug 2022 14:40:57: 10000000 INFO @ Tue, 02 Aug 2022 14:41:00: 7000000 INFO @ Tue, 02 Aug 2022 14:41:05: 13000000 INFO @ Tue, 02 Aug 2022 14:41:09: 11000000 INFO @ Tue, 02 Aug 2022 14:41:13: 8000000 INFO @ Tue, 02 Aug 2022 14:41:18: 14000000 INFO @ Tue, 02 Aug 2022 14:41:22: 12000000 INFO @ Tue, 02 Aug 2022 14:41:27: 9000000 INFO @ Tue, 02 Aug 2022 14:41:31: 15000000 INFO @ Tue, 02 Aug 2022 14:41:35: 13000000 INFO @ Tue, 02 Aug 2022 14:41:40: 10000000 INFO @ Tue, 02 Aug 2022 14:41:43: 16000000 INFO @ Tue, 02 Aug 2022 14:41:46: 14000000 INFO @ Tue, 02 Aug 2022 14:41:53: 11000000 INFO @ Tue, 02 Aug 2022 14:41:55: 17000000 INFO @ Tue, 02 Aug 2022 14:41:58: 15000000 INFO @ Tue, 02 Aug 2022 14:42:06: 12000000 INFO @ Tue, 02 Aug 2022 14:42:07: 18000000 INFO @ Tue, 02 Aug 2022 14:42:11: 16000000 INFO @ Tue, 02 Aug 2022 14:42:17: 13000000 INFO @ Tue, 02 Aug 2022 14:42:18: 19000000 INFO @ Tue, 02 Aug 2022 14:42:21: 17000000 INFO @ Tue, 02 Aug 2022 14:42:30: 14000000 INFO @ Tue, 02 Aug 2022 14:42:31: 20000000 INFO @ Tue, 02 Aug 2022 14:42:35: 18000000 INFO @ Tue, 02 Aug 2022 14:42:44: 15000000 INFO @ Tue, 02 Aug 2022 14:42:44: 21000000 INFO @ Tue, 02 Aug 2022 14:42:48: 19000000 INFO @ Tue, 02 Aug 2022 14:42:57: 16000000 INFO @ Tue, 02 Aug 2022 14:42:59: 22000000 INFO @ Tue, 02 Aug 2022 14:43:03: 20000000 INFO @ Tue, 02 Aug 2022 14:43:10: 17000000 INFO @ Tue, 02 Aug 2022 14:43:12: 23000000 INFO @ Tue, 02 Aug 2022 14:43:16: 21000000 INFO @ Tue, 02 Aug 2022 14:43:23: 18000000 INFO @ Tue, 02 Aug 2022 14:43:26: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:43:29: 22000000 INFO @ Tue, 02 Aug 2022 14:43:36: 19000000 INFO @ Tue, 02 Aug 2022 14:43:38: 25000000 INFO @ Tue, 02 Aug 2022 14:43:42: 23000000 INFO @ Tue, 02 Aug 2022 14:43:49: 20000000 INFO @ Tue, 02 Aug 2022 14:43:51: 26000000 INFO @ Tue, 02 Aug 2022 14:43:54: 24000000 INFO @ Tue, 02 Aug 2022 14:44:03: 21000000 INFO @ Tue, 02 Aug 2022 14:44:04: 27000000 INFO @ Tue, 02 Aug 2022 14:44:07: 25000000 INFO @ Tue, 02 Aug 2022 14:44:16: 22000000 INFO @ Tue, 02 Aug 2022 14:44:17: 28000000 INFO @ Tue, 02 Aug 2022 14:44:19: 26000000 INFO @ Tue, 02 Aug 2022 14:44:28: 23000000 INFO @ Tue, 02 Aug 2022 14:44:29: 29000000 INFO @ Tue, 02 Aug 2022 14:44:32: 27000000 INFO @ Tue, 02 Aug 2022 14:44:42: 30000000 INFO @ Tue, 02 Aug 2022 14:44:42: 24000000 INFO @ Tue, 02 Aug 2022 14:44:45: 28000000 INFO @ Tue, 02 Aug 2022 14:44:55: 31000000 INFO @ Tue, 02 Aug 2022 14:44:55: 25000000 INFO @ Tue, 02 Aug 2022 14:44:58: 29000000 INFO @ Tue, 02 Aug 2022 14:45:06: 32000000 INFO @ Tue, 02 Aug 2022 14:45:07: 26000000 INFO @ Tue, 02 Aug 2022 14:45:08: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:45:08: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:45:08: #1 total tags in treatment: 32129029 INFO @ Tue, 02 Aug 2022 14:45:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:45:08: #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 14:45:09: #1 tags after filtering in treatment: 32129029 INFO @ Tue, 02 Aug 2022 14:45:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:45:09: #1 finished! INFO @ Tue, 02 Aug 2022 14:45:09: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:45:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:45:10: 30000000 INFO @ Tue, 02 Aug 2022 14:45:12: #2 number of paired peaks: 113 WARNING @ Tue, 02 Aug 2022 14:45:12: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 02 Aug 2022 14:45:12: start model_add_line... INFO @ Tue, 02 Aug 2022 14:45:12: start X-correlation... INFO @ Tue, 02 Aug 2022 14:45:12: end of X-cor INFO @ Tue, 02 Aug 2022 14:45:12: #2 finished! INFO @ Tue, 02 Aug 2022 14:45:12: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 14:45:12: #2 alternative fragment length(s) may be 1,72,507,524,551,580 bps INFO @ Tue, 02 Aug 2022 14:45:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.05_model.r WARNING @ Tue, 02 Aug 2022 14:45:12: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:45:12: #2 You may need to consider one of the other alternative d(s): 1,72,507,524,551,580 WARNING @ Tue, 02 Aug 2022 14:45:12: #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 14:45:12: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:45:12: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:45:20: 27000000 INFO @ Tue, 02 Aug 2022 14:45:22: 31000000 INFO @ Tue, 02 Aug 2022 14:45:34: 32000000 INFO @ Tue, 02 Aug 2022 14:45:34: 28000000 INFO @ Tue, 02 Aug 2022 14:45:35: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:45:35: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:45:35: #1 total tags in treatment: 32129029 INFO @ Tue, 02 Aug 2022 14:45:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:45:35: #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 14:45:36: #1 tags after filtering in treatment: 32129029 INFO @ Tue, 02 Aug 2022 14:45:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:45:36: #1 finished! INFO @ Tue, 02 Aug 2022 14:45:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:45:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:45:39: #2 number of paired peaks: 113 WARNING @ Tue, 02 Aug 2022 14:45:39: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 02 Aug 2022 14:45:39: start model_add_line... INFO @ Tue, 02 Aug 2022 14:45:39: start X-correlation... INFO @ Tue, 02 Aug 2022 14:45:39: end of X-cor INFO @ Tue, 02 Aug 2022 14:45:39: #2 finished! INFO @ Tue, 02 Aug 2022 14:45:39: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 14:45:39: #2 alternative fragment length(s) may be 1,72,507,524,551,580 bps INFO @ Tue, 02 Aug 2022 14:45:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.10_model.r WARNING @ Tue, 02 Aug 2022 14:45:39: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:45:39: #2 You may need to consider one of the other alternative d(s): 1,72,507,524,551,580 WARNING @ Tue, 02 Aug 2022 14:45:39: #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 14:45:39: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:45:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:45:45: 29000000 INFO @ Tue, 02 Aug 2022 14:45:58: 30000000 INFO @ Tue, 02 Aug 2022 14:46:10: 31000000 INFO @ Tue, 02 Aug 2022 14:46:21: 32000000 INFO @ Tue, 02 Aug 2022 14:46:23: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 14:46:23: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 14:46:23: #1 total tags in treatment: 32129029 INFO @ Tue, 02 Aug 2022 14:46:23: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:46:23: #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 14:46:23: #1 tags after filtering in treatment: 32129029 INFO @ Tue, 02 Aug 2022 14:46:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:46:23: #1 finished! INFO @ Tue, 02 Aug 2022 14:46:23: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:46:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:46:25: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:46:26: #2 number of paired peaks: 113 WARNING @ Tue, 02 Aug 2022 14:46:26: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 02 Aug 2022 14:46:26: start model_add_line... INFO @ Tue, 02 Aug 2022 14:46:26: start X-correlation... INFO @ Tue, 02 Aug 2022 14:46:26: end of X-cor INFO @ Tue, 02 Aug 2022 14:46:26: #2 finished! INFO @ Tue, 02 Aug 2022 14:46:26: #2 predicted fragment length is 72 bps INFO @ Tue, 02 Aug 2022 14:46:26: #2 alternative fragment length(s) may be 1,72,507,524,551,580 bps INFO @ Tue, 02 Aug 2022 14:46:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.20_model.r WARNING @ Tue, 02 Aug 2022 14:46:26: #2 Since the d (72) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:46:26: #2 You may need to consider one of the other alternative d(s): 1,72,507,524,551,580 WARNING @ Tue, 02 Aug 2022 14:46:26: #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 14:46:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:46:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:46:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:47:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:47:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:47:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.05_summits.bed INFO @ Tue, 02 Aug 2022 14:47:05: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1178 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:47:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:47:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:47:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.10_summits.bed INFO @ Tue, 02 Aug 2022 14:47:31: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (632 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:47:39: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:48:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:48:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:48:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10031694/SRX10031694.20_summits.bed INFO @ Tue, 02 Aug 2022 14:48:18: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (304 records, 4 fields): 15 millis CompletedMACS2peakCalling