Job ID = 6627294 SRX = SRX8521357 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:53:44 prefetch.2.10.7: 1) Downloading 'SRR11978082'... 2020-07-14T01:53:44 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:56:39 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:56:39 prefetch.2.10.7: 1) 'SRR11978082' was downloaded successfully 2020-07-14T01:56:39 prefetch.2.10.7: 'SRR11978082' has 0 unresolved dependencies Read 19563827 spots for SRR11978082/SRR11978082.sra Written 19563827 spots for SRR11978082/SRR11978082.sra 2020-07-14T01:57:56 prefetch.2.10.7: 1) Downloading 'SRR11978083'... 2020-07-14T01:57:56 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:00:39 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:00:39 prefetch.2.10.7: 1) 'SRR11978083' was downloaded successfully 2020-07-14T02:00:39 prefetch.2.10.7: 'SRR11978083' has 0 unresolved dependencies Read 18983150 spots for SRR11978083/SRR11978083.sra Written 18983150 spots for SRR11978083/SRR11978083.sra 2020-07-14T02:01:57 prefetch.2.10.7: 1) Downloading 'SRR11978084'... 2020-07-14T02:01:57 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:03:58 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:03:58 prefetch.2.10.7: 1) 'SRR11978084' was downloaded successfully 2020-07-14T02:03:58 prefetch.2.10.7: 'SRR11978084' has 0 unresolved dependencies Read 19739006 spots for SRR11978084/SRR11978084.sra Written 19739006 spots for SRR11978084/SRR11978084.sra 2020-07-14T02:05:13 prefetch.2.10.7: 1) Downloading 'SRR11978085'... 2020-07-14T02:05:13 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:06:53 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:06:53 prefetch.2.10.7: 1) 'SRR11978085' was downloaded successfully 2020-07-14T02:06:53 prefetch.2.10.7: 'SRR11978085' has 0 unresolved dependencies Read 19625048 spots for SRR11978085/SRR11978085.sra Written 19625048 spots for SRR11978085/SRR11978085.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627571 ("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: 00:14:41 77911031 reads; of these: 77911031 (100.00%) were unpaired; of these: 63799119 (81.89%) aligned 0 times 9317945 (11.96%) aligned exactly 1 time 4793967 (6.15%) aligned >1 times 18.11% overall alignment rate Time searching: 00:14:41 Overall time: 00:14:41 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] 3654699 / 14111912 = 0.2590 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 11:27:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.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 11:27:35: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:27:35: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:27:41: 1000000 INFO @ Tue, 14 Jul 2020 11:27:47: 2000000 INFO @ Tue, 14 Jul 2020 11:27:53: 3000000 INFO @ Tue, 14 Jul 2020 11:27:59: 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 11:28:05: 5000000 INFO @ Tue, 14 Jul 2020 11:28:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.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 11:28:05: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:28:05: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:28:11: 6000000 INFO @ Tue, 14 Jul 2020 11:28:12: 1000000 INFO @ Tue, 14 Jul 2020 11:28:18: 7000000 INFO @ Tue, 14 Jul 2020 11:28:19: 2000000 INFO @ Tue, 14 Jul 2020 11:28:25: 8000000 INFO @ Tue, 14 Jul 2020 11:28:26: 3000000 INFO @ Tue, 14 Jul 2020 11:28:32: 9000000 INFO @ Tue, 14 Jul 2020 11:28:32: 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 11:28:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.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 11:28:35: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:28:35: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:28:39: 10000000 INFO @ Tue, 14 Jul 2020 11:28:39: 5000000 INFO @ Tue, 14 Jul 2020 11:28:42: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 11:28:42: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 11:28:42: #1 total tags in treatment: 10457213 INFO @ Tue, 14 Jul 2020 11:28:42: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:28:42: #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 11:28:42: #1 tags after filtering in treatment: 10457213 INFO @ Tue, 14 Jul 2020 11:28:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:28:42: #1 finished! INFO @ Tue, 14 Jul 2020 11:28:42: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:28:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:28:42: 1000000 INFO @ Tue, 14 Jul 2020 11:28:43: #2 number of paired peaks: 103 WARNING @ Tue, 14 Jul 2020 11:28:43: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Tue, 14 Jul 2020 11:28:43: start model_add_line... INFO @ Tue, 14 Jul 2020 11:28:43: start X-correlation... INFO @ Tue, 14 Jul 2020 11:28:43: end of X-cor INFO @ Tue, 14 Jul 2020 11:28:43: #2 finished! INFO @ Tue, 14 Jul 2020 11:28:43: #2 predicted fragment length is 54 bps INFO @ Tue, 14 Jul 2020 11:28:43: #2 alternative fragment length(s) may be 54,514 bps INFO @ Tue, 14 Jul 2020 11:28:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.05_model.r WARNING @ Tue, 14 Jul 2020 11:28:43: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:28:43: #2 You may need to consider one of the other alternative d(s): 54,514 WARNING @ Tue, 14 Jul 2020 11:28:43: #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 11:28:43: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:28:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:28:46: 6000000 INFO @ Tue, 14 Jul 2020 11:28:49: 2000000 INFO @ Tue, 14 Jul 2020 11:28:53: 7000000 INFO @ Tue, 14 Jul 2020 11:28:56: 3000000 INFO @ Tue, 14 Jul 2020 11:28:59: 8000000 INFO @ Tue, 14 Jul 2020 11:29:02: 4000000 INFO @ Tue, 14 Jul 2020 11:29:04: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:29:06: 9000000 INFO @ Tue, 14 Jul 2020 11:29:09: 5000000 INFO @ Tue, 14 Jul 2020 11:29:13: 10000000 INFO @ Tue, 14 Jul 2020 11:29:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:29:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:29:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.05_summits.bed INFO @ Tue, 14 Jul 2020 11:29:14: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1955 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:29:16: 6000000 INFO @ Tue, 14 Jul 2020 11:29:16: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 11:29:16: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 11:29:16: #1 total tags in treatment: 10457213 INFO @ Tue, 14 Jul 2020 11:29:16: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:29:16: #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 11:29:16: #1 tags after filtering in treatment: 10457213 INFO @ Tue, 14 Jul 2020 11:29:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:29:16: #1 finished! INFO @ Tue, 14 Jul 2020 11:29:16: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:29:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:29:17: #2 number of paired peaks: 103 WARNING @ Tue, 14 Jul 2020 11:29:17: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Tue, 14 Jul 2020 11:29:17: start model_add_line... INFO @ Tue, 14 Jul 2020 11:29:17: start X-correlation... INFO @ Tue, 14 Jul 2020 11:29:17: end of X-cor INFO @ Tue, 14 Jul 2020 11:29:17: #2 finished! INFO @ Tue, 14 Jul 2020 11:29:17: #2 predicted fragment length is 54 bps INFO @ Tue, 14 Jul 2020 11:29:17: #2 alternative fragment length(s) may be 54,514 bps INFO @ Tue, 14 Jul 2020 11:29:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.10_model.r WARNING @ Tue, 14 Jul 2020 11:29:17: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:29:17: #2 You may need to consider one of the other alternative d(s): 54,514 WARNING @ Tue, 14 Jul 2020 11:29:17: #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 11:29:17: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:29:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:29:22: 7000000 INFO @ Tue, 14 Jul 2020 11:29:28: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:29:34: 9000000 INFO @ Tue, 14 Jul 2020 11:29:38: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:29:40: 10000000 INFO @ Tue, 14 Jul 2020 11:29:43: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 11:29:43: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 11:29:43: #1 total tags in treatment: 10457213 INFO @ Tue, 14 Jul 2020 11:29:43: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:29:43: #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 11:29:43: #1 tags after filtering in treatment: 10457213 INFO @ Tue, 14 Jul 2020 11:29:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:29:43: #1 finished! INFO @ Tue, 14 Jul 2020 11:29:43: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:29:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:29:43: #2 number of paired peaks: 103 WARNING @ Tue, 14 Jul 2020 11:29:43: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Tue, 14 Jul 2020 11:29:43: start model_add_line... INFO @ Tue, 14 Jul 2020 11:29:43: start X-correlation... INFO @ Tue, 14 Jul 2020 11:29:43: end of X-cor INFO @ Tue, 14 Jul 2020 11:29:43: #2 finished! INFO @ Tue, 14 Jul 2020 11:29:43: #2 predicted fragment length is 54 bps INFO @ Tue, 14 Jul 2020 11:29:43: #2 alternative fragment length(s) may be 54,514 bps INFO @ Tue, 14 Jul 2020 11:29:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.20_model.r WARNING @ Tue, 14 Jul 2020 11:29:43: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:29:43: #2 You may need to consider one of the other alternative d(s): 54,514 WARNING @ Tue, 14 Jul 2020 11:29:43: #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 11:29:43: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:29:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:29:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:29:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:29:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.10_summits.bed INFO @ Tue, 14 Jul 2020 11:29:48: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1054 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:30:04: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:30:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:30:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:30:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521357/SRX8521357.20_summits.bed INFO @ Tue, 14 Jul 2020 11:30:15: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (347 records, 4 fields): 1 millis CompletedMACS2peakCalling