Job ID = 6627482 SRX = SRX8521394 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T02:45:13 prefetch.2.10.7: 1) Downloading 'SRR11978318'... 2020-07-14T02:45:13 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:47:17 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:47:18 prefetch.2.10.7: 'SRR11978318' is valid 2020-07-14T02:47:18 prefetch.2.10.7: 1) 'SRR11978318' was downloaded successfully 2020-07-14T02:47:18 prefetch.2.10.7: 'SRR11978318' has 0 unresolved dependencies Read 12461394 spots for SRR11978318/SRR11978318.sra Written 12461394 spots for SRR11978318/SRR11978318.sra 2020-07-14T02:48:12 prefetch.2.10.7: 1) Downloading 'SRR11978319'... 2020-07-14T02:48:12 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:49:23 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:49:24 prefetch.2.10.7: 'SRR11978319' is valid 2020-07-14T02:49:24 prefetch.2.10.7: 1) 'SRR11978319' was downloaded successfully 2020-07-14T02:49:24 prefetch.2.10.7: 'SRR11978319' has 0 unresolved dependencies Read 12438853 spots for SRR11978319/SRR11978319.sra Written 12438853 spots for SRR11978319/SRR11978319.sra 2020-07-14T02:50:15 prefetch.2.10.7: 1) Downloading 'SRR11978320'... 2020-07-14T02:50:15 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:51:22 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:51:22 prefetch.2.10.7: 'SRR11978320' is valid 2020-07-14T02:51:22 prefetch.2.10.7: 1) 'SRR11978320' was downloaded successfully 2020-07-14T02:51:22 prefetch.2.10.7: 'SRR11978320' has 0 unresolved dependencies Read 12622672 spots for SRR11978320/SRR11978320.sra Written 12622672 spots for SRR11978320/SRR11978320.sra 2020-07-14T02:52:18 prefetch.2.10.7: 1) Downloading 'SRR11978321'... 2020-07-14T02:52:18 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:54:16 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:54:16 prefetch.2.10.7: 'SRR11978321' is valid 2020-07-14T02:54:16 prefetch.2.10.7: 1) 'SRR11978321' was downloaded successfully 2020-07-14T02:54:16 prefetch.2.10.7: 'SRR11978321' has 0 unresolved dependencies Read 12622200 spots for SRR11978321/SRR11978321.sra Written 12622200 spots for SRR11978321/SRR11978321.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627692 ("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: 00:06:47 50145119 reads; of these: 50145119 (100.00%) were unpaired; of these: 43333581 (86.42%) aligned 0 times 5231066 (10.43%) aligned exactly 1 time 1580472 (3.15%) aligned >1 times 13.58% overall alignment rate Time searching: 00:06:47 Overall time: 00:06:47 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_rmdupse_core] 1043663 / 6811538 = 0.1532 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 12:04:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.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 12:04:21: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:04:21: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:04:27: 1000000 INFO @ Tue, 14 Jul 2020 12:04:32: 2000000 INFO @ Tue, 14 Jul 2020 12:04:37: 3000000 INFO @ Tue, 14 Jul 2020 12:04:42: 4000000 INFO @ Tue, 14 Jul 2020 12:04:47: 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, 14 Jul 2020 12:04:50: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 12:04:50: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 12:04:50: #1 total tags in treatment: 5767875 INFO @ Tue, 14 Jul 2020 12:04:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:04:50: #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 12:04:51: #1 tags after filtering in treatment: 5767875 INFO @ Tue, 14 Jul 2020 12:04:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:04:51: #1 finished! INFO @ Tue, 14 Jul 2020 12:04:51: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:04:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:04:51: #2 number of paired peaks: 309 WARNING @ Tue, 14 Jul 2020 12:04:51: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Tue, 14 Jul 2020 12:04:51: start model_add_line... INFO @ Tue, 14 Jul 2020 12:04:51: start X-correlation... INFO @ Tue, 14 Jul 2020 12:04:51: end of X-cor INFO @ Tue, 14 Jul 2020 12:04:51: #2 finished! INFO @ Tue, 14 Jul 2020 12:04:51: #2 predicted fragment length is 51 bps INFO @ Tue, 14 Jul 2020 12:04:51: #2 alternative fragment length(s) may be 51,557 bps INFO @ Tue, 14 Jul 2020 12:04:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.05_model.r WARNING @ Tue, 14 Jul 2020 12:04:51: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:04:51: #2 You may need to consider one of the other alternative d(s): 51,557 WARNING @ Tue, 14 Jul 2020 12:04:51: #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 12:04:51: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:04:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:04:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.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 12:04:51: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:04:51: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:04:57: 1000000 INFO @ Tue, 14 Jul 2020 12:05:02: 2000000 INFO @ Tue, 14 Jul 2020 12:05:03: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:05:07: 3000000 INFO @ Tue, 14 Jul 2020 12:05:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:05:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:05:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.05_summits.bed INFO @ Tue, 14 Jul 2020 12:05:09: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1588 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:05:12: 4000000 INFO @ Tue, 14 Jul 2020 12:05:17: 5000000 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 12:05:21: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 12:05:21: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 12:05:21: #1 total tags in treatment: 5767875 INFO @ Tue, 14 Jul 2020 12:05:21: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:05:21: #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 12:05:21: #1 tags after filtering in treatment: 5767875 INFO @ Tue, 14 Jul 2020 12:05:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:05:21: #1 finished! INFO @ Tue, 14 Jul 2020 12:05:21: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:05:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:05:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.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 12:05:21: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:05:21: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:05:22: #2 number of paired peaks: 309 WARNING @ Tue, 14 Jul 2020 12:05:22: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Tue, 14 Jul 2020 12:05:22: start model_add_line... INFO @ Tue, 14 Jul 2020 12:05:22: start X-correlation... INFO @ Tue, 14 Jul 2020 12:05:22: end of X-cor INFO @ Tue, 14 Jul 2020 12:05:22: #2 finished! INFO @ Tue, 14 Jul 2020 12:05:22: #2 predicted fragment length is 51 bps INFO @ Tue, 14 Jul 2020 12:05:22: #2 alternative fragment length(s) may be 51,557 bps INFO @ Tue, 14 Jul 2020 12:05:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.10_model.r WARNING @ Tue, 14 Jul 2020 12:05:22: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:05:22: #2 You may need to consider one of the other alternative d(s): 51,557 WARNING @ Tue, 14 Jul 2020 12:05:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:05:22: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:05:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:05:27: 1000000 INFO @ Tue, 14 Jul 2020 12:05:32: 2000000 INFO @ Tue, 14 Jul 2020 12:05:34: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:05:37: 3000000 INFO @ Tue, 14 Jul 2020 12:05:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:05:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:05:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.10_summits.bed INFO @ Tue, 14 Jul 2020 12:05:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (693 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:05:42: 4000000 INFO @ Tue, 14 Jul 2020 12:05:47: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:05:50: #1 tag size is determined as 51 bps INFO @ Tue, 14 Jul 2020 12:05:50: #1 tag size = 51 INFO @ Tue, 14 Jul 2020 12:05:50: #1 total tags in treatment: 5767875 INFO @ Tue, 14 Jul 2020 12:05:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:05:50: #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 12:05:51: #1 tags after filtering in treatment: 5767875 INFO @ Tue, 14 Jul 2020 12:05:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:05:51: #1 finished! INFO @ Tue, 14 Jul 2020 12:05:51: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:05:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:05:51: #2 number of paired peaks: 309 WARNING @ Tue, 14 Jul 2020 12:05:51: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Tue, 14 Jul 2020 12:05:51: start model_add_line... INFO @ Tue, 14 Jul 2020 12:05:51: start X-correlation... INFO @ Tue, 14 Jul 2020 12:05:51: end of X-cor INFO @ Tue, 14 Jul 2020 12:05:51: #2 finished! INFO @ Tue, 14 Jul 2020 12:05:51: #2 predicted fragment length is 51 bps INFO @ Tue, 14 Jul 2020 12:05:51: #2 alternative fragment length(s) may be 51,557 bps INFO @ Tue, 14 Jul 2020 12:05:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.20_model.r WARNING @ Tue, 14 Jul 2020 12:05:51: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:05:51: #2 You may need to consider one of the other alternative d(s): 51,557 WARNING @ Tue, 14 Jul 2020 12:05:51: #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 12:05:51: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:05:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:06:03: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:06:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:06:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:06:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521394/SRX8521394.20_summits.bed INFO @ Tue, 14 Jul 2020 12:06:09: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (99 records, 4 fields): 2 millis CompletedMACS2peakCalling