Job ID = 6627575 SRX = SRX8521409 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T03:03:14 prefetch.2.10.7: 1) Downloading 'SRR11978378'... 2020-07-14T03:03:14 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:05:43 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:05:44 prefetch.2.10.7: 'SRR11978378' is valid 2020-07-14T03:05:44 prefetch.2.10.7: 1) 'SRR11978378' was downloaded successfully 2020-07-14T03:05:44 prefetch.2.10.7: 'SRR11978378' has 0 unresolved dependencies Read 13579387 spots for SRR11978378/SRR11978378.sra Written 13579387 spots for SRR11978378/SRR11978378.sra 2020-07-14T03:06:41 prefetch.2.10.7: 1) Downloading 'SRR11978379'... 2020-07-14T03:06:41 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:08:06 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:08:07 prefetch.2.10.7: 'SRR11978379' is valid 2020-07-14T03:08:07 prefetch.2.10.7: 1) 'SRR11978379' was downloaded successfully 2020-07-14T03:08:07 prefetch.2.10.7: 'SRR11978379' has 0 unresolved dependencies Read 13447878 spots for SRR11978379/SRR11978379.sra Written 13447878 spots for SRR11978379/SRR11978379.sra 2020-07-14T03:09:05 prefetch.2.10.7: 1) Downloading 'SRR11978380'... 2020-07-14T03:09:05 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:10:19 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:10:19 prefetch.2.10.7: 'SRR11978380' is valid 2020-07-14T03:10:19 prefetch.2.10.7: 1) 'SRR11978380' was downloaded successfully 2020-07-14T03:10:19 prefetch.2.10.7: 'SRR11978380' has 0 unresolved dependencies Read 13630463 spots for SRR11978380/SRR11978380.sra Written 13630463 spots for SRR11978380/SRR11978380.sra 2020-07-14T03:11:17 prefetch.2.10.7: 1) Downloading 'SRR11978381'... 2020-07-14T03:11:17 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:13:22 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:13:23 prefetch.2.10.7: 'SRR11978381' is valid 2020-07-14T03:13:23 prefetch.2.10.7: 1) 'SRR11978381' was downloaded successfully 2020-07-14T03:13:23 prefetch.2.10.7: 'SRR11978381' has 0 unresolved dependencies Read 13578449 spots for SRR11978381/SRR11978381.sra Written 13578449 spots for SRR11978381/SRR11978381.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627768 ("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: 00:06:46 54236177 reads; of these: 54236177 (100.00%) were unpaired; of these: 48519320 (89.46%) aligned 0 times 4341959 (8.01%) aligned exactly 1 time 1374898 (2.54%) aligned >1 times 10.54% overall alignment rate Time searching: 00:06:46 Overall time: 00:06:46 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] 1003037 / 5716857 = 0.1755 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 12:23:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.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 12:23:19: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:23:19: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:23:24: 1000000 INFO @ Tue, 14 Jul 2020 12:23:30: 2000000 INFO @ Tue, 14 Jul 2020 12:23:36: 3000000 INFO @ Tue, 14 Jul 2020 12:23:41: 4000000 INFO @ Tue, 14 Jul 2020 12:23:45: #1 tag size is determined as 58 bps INFO @ Tue, 14 Jul 2020 12:23:45: #1 tag size = 58 INFO @ Tue, 14 Jul 2020 12:23:45: #1 total tags in treatment: 4713820 INFO @ Tue, 14 Jul 2020 12:23:45: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:23:45: #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 12:23:45: #1 tags after filtering in treatment: 4713820 INFO @ Tue, 14 Jul 2020 12:23:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:23:45: #1 finished! INFO @ Tue, 14 Jul 2020 12:23:45: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:23:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:23:46: #2 number of paired peaks: 442 WARNING @ Tue, 14 Jul 2020 12:23:46: Fewer paired peaks (442) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 442 pairs to build model! INFO @ Tue, 14 Jul 2020 12:23:46: start model_add_line... INFO @ Tue, 14 Jul 2020 12:23:46: start X-correlation... INFO @ Tue, 14 Jul 2020 12:23:46: end of X-cor INFO @ Tue, 14 Jul 2020 12:23:46: #2 finished! INFO @ Tue, 14 Jul 2020 12:23:46: #2 predicted fragment length is 54 bps INFO @ Tue, 14 Jul 2020 12:23:46: #2 alternative fragment length(s) may be 54 bps INFO @ Tue, 14 Jul 2020 12:23:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.05_model.r WARNING @ Tue, 14 Jul 2020 12:23:46: #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 12:23:46: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Tue, 14 Jul 2020 12:23:46: #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 12:23:46: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:23:46: #3 Pre-compute pvalue-qvalue table... 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 12:23:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.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 12:23:49: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:23:49: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:23:55: 1000000 INFO @ Tue, 14 Jul 2020 12:23:55: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:24:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:24:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:24:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.05_summits.bed INFO @ Tue, 14 Jul 2020 12:24:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1598 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:24:01: 2000000 INFO @ Tue, 14 Jul 2020 12:24:07: 3000000 INFO @ Tue, 14 Jul 2020 12:24:13: 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 12:24:18: #1 tag size is determined as 58 bps INFO @ Tue, 14 Jul 2020 12:24:18: #1 tag size = 58 INFO @ Tue, 14 Jul 2020 12:24:18: #1 total tags in treatment: 4713820 INFO @ Tue, 14 Jul 2020 12:24:18: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:24:18: #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 12:24:18: #1 tags after filtering in treatment: 4713820 INFO @ Tue, 14 Jul 2020 12:24:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:24:18: #1 finished! INFO @ Tue, 14 Jul 2020 12:24:18: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:24:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:24:18: #2 number of paired peaks: 442 WARNING @ Tue, 14 Jul 2020 12:24:18: Fewer paired peaks (442) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 442 pairs to build model! INFO @ Tue, 14 Jul 2020 12:24:18: start model_add_line... INFO @ Tue, 14 Jul 2020 12:24:18: start X-correlation... INFO @ Tue, 14 Jul 2020 12:24:18: end of X-cor INFO @ Tue, 14 Jul 2020 12:24:18: #2 finished! INFO @ Tue, 14 Jul 2020 12:24:18: #2 predicted fragment length is 54 bps INFO @ Tue, 14 Jul 2020 12:24:18: #2 alternative fragment length(s) may be 54 bps INFO @ Tue, 14 Jul 2020 12:24:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.10_model.r WARNING @ Tue, 14 Jul 2020 12:24:18: #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 12:24:18: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Tue, 14 Jul 2020 12:24:18: #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 12:24:18: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:24:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:24:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.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 12:24:19: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:24:19: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:24:26: 1000000 INFO @ Tue, 14 Jul 2020 12:24:28: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:24:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:24:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:24:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.10_summits.bed INFO @ Tue, 14 Jul 2020 12:24:33: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (692 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:24:33: 2000000 INFO @ Tue, 14 Jul 2020 12:24:40: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:24:47: 4000000 INFO @ Tue, 14 Jul 2020 12:24:52: #1 tag size is determined as 58 bps INFO @ Tue, 14 Jul 2020 12:24:52: #1 tag size = 58 INFO @ Tue, 14 Jul 2020 12:24:52: #1 total tags in treatment: 4713820 INFO @ Tue, 14 Jul 2020 12:24:52: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:24:52: #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 12:24:52: #1 tags after filtering in treatment: 4713820 INFO @ Tue, 14 Jul 2020 12:24:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:24:52: #1 finished! INFO @ Tue, 14 Jul 2020 12:24:52: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:24:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:24:53: #2 number of paired peaks: 442 WARNING @ Tue, 14 Jul 2020 12:24:53: Fewer paired peaks (442) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 442 pairs to build model! INFO @ Tue, 14 Jul 2020 12:24:53: start model_add_line... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:24:53: start X-correlation... INFO @ Tue, 14 Jul 2020 12:24:53: end of X-cor INFO @ Tue, 14 Jul 2020 12:24:53: #2 finished! INFO @ Tue, 14 Jul 2020 12:24:53: #2 predicted fragment length is 54 bps INFO @ Tue, 14 Jul 2020 12:24:53: #2 alternative fragment length(s) may be 54 bps INFO @ Tue, 14 Jul 2020 12:24:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.20_model.r WARNING @ Tue, 14 Jul 2020 12:24:53: #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 12:24:53: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Tue, 14 Jul 2020 12:24:53: #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 12:24:53: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:24:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:25:03: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:25:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:25:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:25:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521409/SRX8521409.20_summits.bed INFO @ Tue, 14 Jul 2020 12:25:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (129 records, 4 fields): 1 millis CompletedMACS2peakCalling