Job ID = 6528466 SRX = SRX6827666 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T15:15:21 prefetch.2.10.7: 1) Downloading 'SRR10095446'... 2020-06-29T15:15:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T15:18:41 prefetch.2.10.7: HTTPS download succeed 2020-06-29T15:18:41 prefetch.2.10.7: 1) 'SRR10095446' was downloaded successfully Read 29364739 spots for SRR10095446/SRR10095446.sra Written 29364739 spots for SRR10095446/SRR10095446.sra 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: 00:10:08 29364739 reads; of these: 29364739 (100.00%) were unpaired; of these: 908673 (3.09%) aligned 0 times 19517873 (66.47%) aligned exactly 1 time 8938193 (30.44%) aligned >1 times 96.91% overall alignment rate Time searching: 00:10:08 Overall time: 00:10:08 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 12 files... [bam_rmdupse_core] 4685678 / 28456066 = 0.1647 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 00:41:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.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, 30 Jun 2020 00:41:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:41:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:41:54: 1000000 INFO @ Tue, 30 Jun 2020 00:41:59: 2000000 INFO @ Tue, 30 Jun 2020 00:42:04: 3000000 INFO @ Tue, 30 Jun 2020 00:42:09: 4000000 INFO @ Tue, 30 Jun 2020 00:42:14: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 00:42:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.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, 30 Jun 2020 00:42:19: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:42:19: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:42:19: 6000000 INFO @ Tue, 30 Jun 2020 00:42:24: 1000000 INFO @ Tue, 30 Jun 2020 00:42:25: 7000000 INFO @ Tue, 30 Jun 2020 00:42:30: 2000000 INFO @ Tue, 30 Jun 2020 00:42:30: 8000000 INFO @ Tue, 30 Jun 2020 00:42:35: 3000000 INFO @ Tue, 30 Jun 2020 00:42:35: 9000000 INFO @ Tue, 30 Jun 2020 00:42:40: 4000000 INFO @ Tue, 30 Jun 2020 00:42:40: 10000000 INFO @ Tue, 30 Jun 2020 00:42:45: 5000000 INFO @ Tue, 30 Jun 2020 00:42:45: 11000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 00:42:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.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, 30 Jun 2020 00:42:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 00:42:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 00:42:50: 6000000 INFO @ Tue, 30 Jun 2020 00:42:50: 12000000 INFO @ Tue, 30 Jun 2020 00:42:55: 1000000 INFO @ Tue, 30 Jun 2020 00:42:56: 7000000 INFO @ Tue, 30 Jun 2020 00:42:56: 13000000 INFO @ Tue, 30 Jun 2020 00:43:00: 2000000 INFO @ Tue, 30 Jun 2020 00:43:01: 8000000 INFO @ Tue, 30 Jun 2020 00:43:01: 14000000 INFO @ Tue, 30 Jun 2020 00:43:06: 3000000 INFO @ Tue, 30 Jun 2020 00:43:07: 9000000 INFO @ Tue, 30 Jun 2020 00:43:07: 15000000 INFO @ Tue, 30 Jun 2020 00:43:11: 4000000 INFO @ Tue, 30 Jun 2020 00:43:12: 10000000 INFO @ Tue, 30 Jun 2020 00:43:12: 16000000 INFO @ Tue, 30 Jun 2020 00:43:17: 5000000 INFO @ Tue, 30 Jun 2020 00:43:18: 11000000 INFO @ Tue, 30 Jun 2020 00:43:18: 17000000 INFO @ Tue, 30 Jun 2020 00:43:22: 6000000 INFO @ Tue, 30 Jun 2020 00:43:23: 12000000 INFO @ Tue, 30 Jun 2020 00:43:24: 18000000 INFO @ Tue, 30 Jun 2020 00:43:28: 7000000 INFO @ Tue, 30 Jun 2020 00:43:29: 13000000 INFO @ Tue, 30 Jun 2020 00:43:29: 19000000 INFO @ Tue, 30 Jun 2020 00:43:33: 8000000 INFO @ Tue, 30 Jun 2020 00:43:34: 14000000 INFO @ Tue, 30 Jun 2020 00:43:35: 20000000 INFO @ Tue, 30 Jun 2020 00:43:39: 9000000 INFO @ Tue, 30 Jun 2020 00:43:40: 15000000 INFO @ Tue, 30 Jun 2020 00:43:40: 21000000 INFO @ Tue, 30 Jun 2020 00:43:44: 10000000 INFO @ Tue, 30 Jun 2020 00:43:45: 16000000 INFO @ Tue, 30 Jun 2020 00:43:46: 22000000 INFO @ Tue, 30 Jun 2020 00:43:50: 11000000 INFO @ Tue, 30 Jun 2020 00:43:51: 17000000 INFO @ Tue, 30 Jun 2020 00:43:52: 23000000 INFO @ Tue, 30 Jun 2020 00:43:55: 12000000 INFO @ Tue, 30 Jun 2020 00:43:56: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:43:56: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:43:56: #1 total tags in treatment: 23770388 INFO @ Tue, 30 Jun 2020 00:43:56: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:43:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:43:56: #1 tags after filtering in treatment: 23770388 INFO @ Tue, 30 Jun 2020 00:43:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:43:56: #1 finished! INFO @ Tue, 30 Jun 2020 00:43:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:43:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:43:56: 18000000 INFO @ Tue, 30 Jun 2020 00:43:58: #2 number of paired peaks: 295 WARNING @ Tue, 30 Jun 2020 00:43:58: Fewer paired peaks (295) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 295 pairs to build model! INFO @ Tue, 30 Jun 2020 00:43:58: start model_add_line... INFO @ Tue, 30 Jun 2020 00:43:58: start X-correlation... INFO @ Tue, 30 Jun 2020 00:43:58: end of X-cor INFO @ Tue, 30 Jun 2020 00:43:58: #2 finished! INFO @ Tue, 30 Jun 2020 00:43:58: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 00:43:58: #2 alternative fragment length(s) may be 3,45 bps INFO @ Tue, 30 Jun 2020 00:43:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.05_model.r WARNING @ Tue, 30 Jun 2020 00:43:58: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:43:58: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Tue, 30 Jun 2020 00:43:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:43:58: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:43:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:44:01: 13000000 INFO @ Tue, 30 Jun 2020 00:44:02: 19000000 INFO @ Tue, 30 Jun 2020 00:44:06: 14000000 INFO @ Tue, 30 Jun 2020 00:44:07: 20000000 INFO @ Tue, 30 Jun 2020 00:44:12: 15000000 INFO @ Tue, 30 Jun 2020 00:44:13: 21000000 INFO @ Tue, 30 Jun 2020 00:44:17: 16000000 INFO @ Tue, 30 Jun 2020 00:44:18: 22000000 INFO @ Tue, 30 Jun 2020 00:44:22: 17000000 INFO @ Tue, 30 Jun 2020 00:44:24: 23000000 INFO @ Tue, 30 Jun 2020 00:44:28: 18000000 INFO @ Tue, 30 Jun 2020 00:44:28: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:44:28: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:44:28: #1 total tags in treatment: 23770388 INFO @ Tue, 30 Jun 2020 00:44:28: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:44:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:44:29: #1 tags after filtering in treatment: 23770388 INFO @ Tue, 30 Jun 2020 00:44:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:44:29: #1 finished! INFO @ Tue, 30 Jun 2020 00:44:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:44:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:44:30: #2 number of paired peaks: 295 WARNING @ Tue, 30 Jun 2020 00:44:30: Fewer paired peaks (295) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 295 pairs to build model! INFO @ Tue, 30 Jun 2020 00:44:30: start model_add_line... INFO @ Tue, 30 Jun 2020 00:44:30: start X-correlation... INFO @ Tue, 30 Jun 2020 00:44:30: end of X-cor INFO @ Tue, 30 Jun 2020 00:44:30: #2 finished! INFO @ Tue, 30 Jun 2020 00:44:30: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 00:44:30: #2 alternative fragment length(s) may be 3,45 bps INFO @ Tue, 30 Jun 2020 00:44:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.10_model.r WARNING @ Tue, 30 Jun 2020 00:44:30: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:44:30: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Tue, 30 Jun 2020 00:44:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:44:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:44:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:44:33: 19000000 INFO @ Tue, 30 Jun 2020 00:44:38: 20000000 INFO @ Tue, 30 Jun 2020 00:44:40: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:44:44: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 00:44:49: 22000000 INFO @ Tue, 30 Jun 2020 00:44:55: 23000000 INFO @ Tue, 30 Jun 2020 00:44:59: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 00:44:59: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 00:44:59: #1 total tags in treatment: 23770388 INFO @ Tue, 30 Jun 2020 00:44:59: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 00:44:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 00:44:59: #1 tags after filtering in treatment: 23770388 INFO @ Tue, 30 Jun 2020 00:44:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 00:44:59: #1 finished! INFO @ Tue, 30 Jun 2020 00:44:59: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 00:44:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 00:45:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.05_peaks.xls INFO @ Tue, 30 Jun 2020 00:45:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:45:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.05_summits.bed INFO @ Tue, 30 Jun 2020 00:45:01: Done! INFO @ Tue, 30 Jun 2020 00:45:01: #2 number of paired peaks: 295 WARNING @ Tue, 30 Jun 2020 00:45:01: Fewer paired peaks (295) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 295 pairs to build model! INFO @ Tue, 30 Jun 2020 00:45:01: start model_add_line... pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3605 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 00:45:01: start X-correlation... INFO @ Tue, 30 Jun 2020 00:45:01: end of X-cor INFO @ Tue, 30 Jun 2020 00:45:01: #2 finished! INFO @ Tue, 30 Jun 2020 00:45:01: #2 predicted fragment length is 45 bps INFO @ Tue, 30 Jun 2020 00:45:01: #2 alternative fragment length(s) may be 3,45 bps INFO @ Tue, 30 Jun 2020 00:45:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.20_model.r WARNING @ Tue, 30 Jun 2020 00:45:01: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 00:45:01: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Tue, 30 Jun 2020 00:45:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 00:45:01: #3 Call peaks... INFO @ Tue, 30 Jun 2020 00:45:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 00:45:11: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:45:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.10_peaks.xls INFO @ Tue, 30 Jun 2020 00:45:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:45:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.10_summits.bed INFO @ Tue, 30 Jun 2020 00:45:31: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2451 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 00:45:42: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 00:46:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.20_peaks.xls INFO @ Tue, 30 Jun 2020 00:46:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 00:46:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6827666/SRX6827666.20_summits.bed INFO @ Tue, 30 Jun 2020 00:46:03: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1303 records, 4 fields): 3 millis CompletedMACS2peakCalling