Job ID = 6627479 SRX = SRX8521392 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T02:44:51 prefetch.2.10.7: 1) Downloading 'SRR11978310'... 2020-07-14T02:44:51 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:46:36 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:46:37 prefetch.2.10.7: 'SRR11978310' is valid 2020-07-14T02:46:37 prefetch.2.10.7: 1) 'SRR11978310' was downloaded successfully 2020-07-14T02:46:37 prefetch.2.10.7: 'SRR11978310' has 0 unresolved dependencies Read 19535137 spots for SRR11978310/SRR11978310.sra Written 19535137 spots for SRR11978310/SRR11978310.sra 2020-07-14T02:47:56 prefetch.2.10.7: 1) Downloading 'SRR11978311'... 2020-07-14T02:47:56 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:49:32 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:49:33 prefetch.2.10.7: 'SRR11978311' is valid 2020-07-14T02:49:33 prefetch.2.10.7: 1) 'SRR11978311' was downloaded successfully 2020-07-14T02:49:33 prefetch.2.10.7: 'SRR11978311' has 0 unresolved dependencies Read 19555400 spots for SRR11978311/SRR11978311.sra Written 19555400 spots for SRR11978311/SRR11978311.sra 2020-07-14T02:50:55 prefetch.2.10.7: 1) Downloading 'SRR11978312'... 2020-07-14T02:50:55 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:53:28 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:53:29 prefetch.2.10.7: 'SRR11978312' is valid 2020-07-14T02:53:29 prefetch.2.10.7: 1) 'SRR11978312' was downloaded successfully 2020-07-14T02:53:29 prefetch.2.10.7: 'SRR11978312' has 0 unresolved dependencies Read 19698248 spots for SRR11978312/SRR11978312.sra Written 19698248 spots for SRR11978312/SRR11978312.sra 2020-07-14T02:54:47 prefetch.2.10.7: 1) Downloading 'SRR11978313'... 2020-07-14T02:54:47 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:56:39 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:56:39 prefetch.2.10.7: 'SRR11978313' is valid 2020-07-14T02:56:39 prefetch.2.10.7: 1) 'SRR11978313' was downloaded successfully 2020-07-14T02:56:39 prefetch.2.10.7: 'SRR11978313' has 0 unresolved dependencies Read 19547067 spots for SRR11978313/SRR11978313.sra Written 19547067 spots for SRR11978313/SRR11978313.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627726 ("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: 00:10:55 78335852 reads; of these: 78335852 (100.00%) were unpaired; of these: 67435495 (86.09%) aligned 0 times 8358276 (10.67%) aligned exactly 1 time 2542081 (3.25%) aligned >1 times 13.91% overall alignment rate Time searching: 00:10:55 Overall time: 00:10:55 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 8 files... [bam_rmdupse_core] 2013116 / 10900357 = 0.1847 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, 14 Jul 2020 12:12:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.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, 14 Jul 2020 12:12:34: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:12:34: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:12:39: 1000000 INFO @ Tue, 14 Jul 2020 12:12:45: 2000000 INFO @ Tue, 14 Jul 2020 12:12:50: 3000000 INFO @ Tue, 14 Jul 2020 12:12:57: 4000000 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, 14 Jul 2020 12:13:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.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, 14 Jul 2020 12:13:04: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:13:04: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:13:04: 5000000 INFO @ Tue, 14 Jul 2020 12:13:10: 1000000 INFO @ Tue, 14 Jul 2020 12:13:12: 6000000 INFO @ Tue, 14 Jul 2020 12:13:16: 2000000 INFO @ Tue, 14 Jul 2020 12:13:20: 7000000 INFO @ Tue, 14 Jul 2020 12:13:21: 3000000 INFO @ Tue, 14 Jul 2020 12:13:27: 8000000 INFO @ Tue, 14 Jul 2020 12:13:27: 4000000 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, 14 Jul 2020 12:13:33: 5000000 INFO @ Tue, 14 Jul 2020 12:13:33: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 12:13:33: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 12:13:33: #1 total tags in treatment: 8887241 INFO @ Tue, 14 Jul 2020 12:13:33: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:13:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:13:33: #1 tags after filtering in treatment: 8887241 INFO @ Tue, 14 Jul 2020 12:13:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:13:33: #1 finished! INFO @ Tue, 14 Jul 2020 12:13:33: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:13:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:13:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.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, 14 Jul 2020 12:13:34: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:13:34: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:13:34: #2 number of paired peaks: 200 WARNING @ Tue, 14 Jul 2020 12:13:34: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Tue, 14 Jul 2020 12:13:34: start model_add_line... INFO @ Tue, 14 Jul 2020 12:13:34: start X-correlation... INFO @ Tue, 14 Jul 2020 12:13:34: end of X-cor INFO @ Tue, 14 Jul 2020 12:13:34: #2 finished! INFO @ Tue, 14 Jul 2020 12:13:34: #2 predicted fragment length is 49 bps INFO @ Tue, 14 Jul 2020 12:13:34: #2 alternative fragment length(s) may be 49,532,559 bps INFO @ Tue, 14 Jul 2020 12:13:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.05_model.r WARNING @ Tue, 14 Jul 2020 12:13:34: #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, 14 Jul 2020 12:13:34: #2 You may need to consider one of the other alternative d(s): 49,532,559 WARNING @ Tue, 14 Jul 2020 12:13:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:13:34: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:13:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:13:39: 6000000 INFO @ Tue, 14 Jul 2020 12:13:40: 1000000 INFO @ Tue, 14 Jul 2020 12:13:44: 7000000 INFO @ Tue, 14 Jul 2020 12:13:45: 2000000 INFO @ Tue, 14 Jul 2020 12:13:50: 8000000 INFO @ Tue, 14 Jul 2020 12:13:51: 3000000 INFO @ Tue, 14 Jul 2020 12:13:54: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:13:55: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 12:13:55: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 12:13:55: #1 total tags in treatment: 8887241 INFO @ Tue, 14 Jul 2020 12:13:55: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:13:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:13:55: #1 tags after filtering in treatment: 8887241 INFO @ Tue, 14 Jul 2020 12:13:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:13:55: #1 finished! INFO @ Tue, 14 Jul 2020 12:13:55: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:13:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:13:56: #2 number of paired peaks: 200 WARNING @ Tue, 14 Jul 2020 12:13:56: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Tue, 14 Jul 2020 12:13:56: start model_add_line... INFO @ Tue, 14 Jul 2020 12:13:56: start X-correlation... INFO @ Tue, 14 Jul 2020 12:13:56: end of X-cor INFO @ Tue, 14 Jul 2020 12:13:56: #2 finished! INFO @ Tue, 14 Jul 2020 12:13:56: #2 predicted fragment length is 49 bps INFO @ Tue, 14 Jul 2020 12:13:56: #2 alternative fragment length(s) may be 49,532,559 bps INFO @ Tue, 14 Jul 2020 12:13:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.10_model.r WARNING @ Tue, 14 Jul 2020 12:13:56: #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, 14 Jul 2020 12:13:56: #2 You may need to consider one of the other alternative d(s): 49,532,559 WARNING @ Tue, 14 Jul 2020 12:13:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:13:56: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:13:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:13:57: 4000000 INFO @ Tue, 14 Jul 2020 12:14:03: 5000000 INFO @ Tue, 14 Jul 2020 12:14:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:14:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:14:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.05_summits.bed INFO @ Tue, 14 Jul 2020 12:14:05: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1975 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:14:08: 6000000 INFO @ Tue, 14 Jul 2020 12:14:14: 7000000 INFO @ Tue, 14 Jul 2020 12:14:15: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:14:19: 8000000 INFO @ Tue, 14 Jul 2020 12:14:24: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 12:14:24: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 12:14:24: #1 total tags in treatment: 8887241 INFO @ Tue, 14 Jul 2020 12:14:24: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:14:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:14:24: #1 tags after filtering in treatment: 8887241 INFO @ Tue, 14 Jul 2020 12:14:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:14:24: #1 finished! INFO @ Tue, 14 Jul 2020 12:14:24: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:14:24: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:14:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:14:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:14:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.10_summits.bed INFO @ Tue, 14 Jul 2020 12:14:25: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (916 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:14:25: #2 number of paired peaks: 200 WARNING @ Tue, 14 Jul 2020 12:14:25: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Tue, 14 Jul 2020 12:14:25: start model_add_line... INFO @ Tue, 14 Jul 2020 12:14:25: start X-correlation... INFO @ Tue, 14 Jul 2020 12:14:25: end of X-cor INFO @ Tue, 14 Jul 2020 12:14:25: #2 finished! INFO @ Tue, 14 Jul 2020 12:14:25: #2 predicted fragment length is 49 bps INFO @ Tue, 14 Jul 2020 12:14:25: #2 alternative fragment length(s) may be 49,532,559 bps INFO @ Tue, 14 Jul 2020 12:14:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.20_model.r WARNING @ Tue, 14 Jul 2020 12:14:25: #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, 14 Jul 2020 12:14:25: #2 You may need to consider one of the other alternative d(s): 49,532,559 WARNING @ Tue, 14 Jul 2020 12:14:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:14:25: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:14:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:14:45: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:14:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:14:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:14:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521392/SRX8521392.20_summits.bed INFO @ Tue, 14 Jul 2020 12:14:54: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (227 records, 4 fields): 1 millis CompletedMACS2peakCalling