Job ID = 6627468 SRX = SRX8521389 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T02:40:54 prefetch.2.10.7: 1) Downloading 'SRR11978298'... 2020-07-14T02:40:54 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:42:42 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:42:42 prefetch.2.10.7: 'SRR11978298' is valid 2020-07-14T02:42:42 prefetch.2.10.7: 1) 'SRR11978298' was downloaded successfully 2020-07-14T02:42:42 prefetch.2.10.7: 'SRR11978298' has 0 unresolved dependencies Read 12508370 spots for SRR11978298/SRR11978298.sra Written 12508370 spots for SRR11978298/SRR11978298.sra 2020-07-14T02:43:37 prefetch.2.10.7: 1) Downloading 'SRR11978299'... 2020-07-14T02:43:37 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:44:59 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:45:00 prefetch.2.10.7: 'SRR11978299' is valid 2020-07-14T02:45:00 prefetch.2.10.7: 1) 'SRR11978299' was downloaded successfully 2020-07-14T02:45:00 prefetch.2.10.7: 'SRR11978299' has 0 unresolved dependencies Read 12398714 spots for SRR11978299/SRR11978299.sra Written 12398714 spots for SRR11978299/SRR11978299.sra 2020-07-14T02:45:55 prefetch.2.10.7: 1) Downloading 'SRR11978300'... 2020-07-14T02:45:55 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:47:04 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:47:05 prefetch.2.10.7: 'SRR11978300' is valid 2020-07-14T02:47:05 prefetch.2.10.7: 1) 'SRR11978300' was downloaded successfully 2020-07-14T02:47:05 prefetch.2.10.7: 'SRR11978300' has 0 unresolved dependencies Read 12335906 spots for SRR11978300/SRR11978300.sra Written 12335906 spots for SRR11978300/SRR11978300.sra 2020-07-14T02:48:02 prefetch.2.10.7: 1) Downloading 'SRR11978301'... 2020-07-14T02:48:02 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:03:42 prefetch.2.10.7: HTTPS download failed 2020-07-14T03:03:42 prefetch.2.10.7: 1) failed to download SRR11978301 2020-07-14T03:03:59 prefetch.2.10.7: 1) Downloading 'SRR11978301'... 2020-07-14T03:03:59 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:03:59 prefetch.2.10.7: Continue download of 'SRR11978301' from 341072003 2020-07-14T03:04:04 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:04:04 prefetch.2.10.7: 'SRR11978301' is valid 2020-07-14T03:04:04 prefetch.2.10.7: 1) 'SRR11978301' was downloaded successfully 2020-07-14T03:04:04 prefetch.2.10.7: 'SRR11978301' has 0 unresolved dependencies Read 12475398 spots for SRR11978301/SRR11978301.sra Written 12475398 spots for SRR11978301/SRR11978301.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627736 ("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: 00:06:34 49718388 reads; of these: 49718388 (100.00%) were unpaired; of these: 46114607 (92.75%) aligned 0 times 2659246 (5.35%) aligned exactly 1 time 944535 (1.90%) aligned >1 times 7.25% overall alignment rate Time searching: 00:06:34 Overall time: 00:06:34 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] 714905 / 3603781 = 0.1984 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 12:13:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.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 12:13:02: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:13:02: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:13:09: 1000000 INFO @ Tue, 14 Jul 2020 12:13:15: 2000000 INFO @ Tue, 14 Jul 2020 12:13:20: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 12:13:20: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 12:13:20: #1 total tags in treatment: 2888876 INFO @ Tue, 14 Jul 2020 12:13:20: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:13:20: #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 12:13:20: #1 tags after filtering in treatment: 2888876 INFO @ Tue, 14 Jul 2020 12:13:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:13:20: #1 finished! INFO @ Tue, 14 Jul 2020 12:13:20: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:13:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:13:20: #2 number of paired peaks: 758 WARNING @ Tue, 14 Jul 2020 12:13:20: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Tue, 14 Jul 2020 12:13:20: start model_add_line... INFO @ Tue, 14 Jul 2020 12:13:20: start X-correlation... INFO @ Tue, 14 Jul 2020 12:13:20: end of X-cor INFO @ Tue, 14 Jul 2020 12:13:20: #2 finished! INFO @ Tue, 14 Jul 2020 12:13:20: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 12:13:20: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 12:13:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.05_model.r WARNING @ Tue, 14 Jul 2020 12:13:20: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:13:20: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 12:13:20: #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 12:13:20: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:13:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:13:26: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:13:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:13:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:13:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.05_summits.bed INFO @ Tue, 14 Jul 2020 12:13:30: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1466 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 12:13:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.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 12:13:32: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:13:32: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:13:42: 1000000 INFO @ Tue, 14 Jul 2020 12:13:50: 2000000 INFO @ Tue, 14 Jul 2020 12:13:57: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 12:13:57: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 12:13:57: #1 total tags in treatment: 2888876 INFO @ Tue, 14 Jul 2020 12:13:57: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:13:57: #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 12:13:57: #1 tags after filtering in treatment: 2888876 INFO @ Tue, 14 Jul 2020 12:13:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:13:57: #1 finished! INFO @ Tue, 14 Jul 2020 12:13:57: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:13:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:13:57: #2 number of paired peaks: 758 WARNING @ Tue, 14 Jul 2020 12:13:57: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Tue, 14 Jul 2020 12:13:57: start model_add_line... INFO @ Tue, 14 Jul 2020 12:13:57: start X-correlation... INFO @ Tue, 14 Jul 2020 12:13:57: end of X-cor INFO @ Tue, 14 Jul 2020 12:13:57: #2 finished! INFO @ Tue, 14 Jul 2020 12:13:57: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 12:13:57: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 12:13:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.10_model.r WARNING @ Tue, 14 Jul 2020 12:13:57: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:13:57: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 12:13:57: #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 12:13:57: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:13:57: #3 Pre-compute pvalue-qvalue table... 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 12:14:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.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 12:14:02: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:14:02: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:14:03: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:14:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:14:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:14:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.10_summits.bed INFO @ Tue, 14 Jul 2020 12:14:06: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (641 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:14:09: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:14:17: 2000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:14:23: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 12:14:23: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 12:14:23: #1 total tags in treatment: 2888876 INFO @ Tue, 14 Jul 2020 12:14:23: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:14:23: #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 12:14:23: #1 tags after filtering in treatment: 2888876 INFO @ Tue, 14 Jul 2020 12:14:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:14:23: #1 finished! INFO @ Tue, 14 Jul 2020 12:14:23: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:14:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:14:24: #2 number of paired peaks: 758 WARNING @ Tue, 14 Jul 2020 12:14:24: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Tue, 14 Jul 2020 12:14:24: start model_add_line... INFO @ Tue, 14 Jul 2020 12:14:24: start X-correlation... INFO @ Tue, 14 Jul 2020 12:14:24: end of X-cor INFO @ Tue, 14 Jul 2020 12:14:24: #2 finished! INFO @ Tue, 14 Jul 2020 12:14:24: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 12:14:24: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 12:14:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.20_model.r WARNING @ Tue, 14 Jul 2020 12:14:24: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:14:24: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 12:14:24: #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 12:14:24: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:14:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:14:30: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:14:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:14:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:14:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521389/SRX8521389.20_summits.bed INFO @ Tue, 14 Jul 2020 12:14:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (152 records, 4 fields): 1 millis CompletedMACS2peakCalling