Job ID = 6627292 SRX = SRX8521355 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:52:59 prefetch.2.10.7: 1) Downloading 'SRR11978066'... 2020-07-14T01:52:59 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:53:46 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:53:47 prefetch.2.10.7: 'SRR11978066' is valid 2020-07-14T01:53:47 prefetch.2.10.7: 1) 'SRR11978066' was downloaded successfully 2020-07-14T01:53:47 prefetch.2.10.7: 'SRR11978066' has 0 unresolved dependencies Read 3285016 spots for SRR11978066/SRR11978066.sra Written 3285016 spots for SRR11978066/SRR11978066.sra 2020-07-14T01:54:08 prefetch.2.10.7: 1) Downloading 'SRR11978067'... 2020-07-14T01:54:08 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:54:51 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:54:51 prefetch.2.10.7: 'SRR11978067' is valid 2020-07-14T01:54:51 prefetch.2.10.7: 1) 'SRR11978067' was downloaded successfully 2020-07-14T01:54:51 prefetch.2.10.7: 'SRR11978067' has 0 unresolved dependencies Read 3237941 spots for SRR11978067/SRR11978067.sra Written 3237941 spots for SRR11978067/SRR11978067.sra 2020-07-14T01:55:12 prefetch.2.10.7: 1) Downloading 'SRR11978068'... 2020-07-14T01:55:12 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:55:43 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:55:43 prefetch.2.10.7: 'SRR11978068' is valid 2020-07-14T01:55:43 prefetch.2.10.7: 1) 'SRR11978068' was downloaded successfully 2020-07-14T01:55:43 prefetch.2.10.7: 'SRR11978068' has 0 unresolved dependencies Read 3329372 spots for SRR11978068/SRR11978068.sra Written 3329372 spots for SRR11978068/SRR11978068.sra 2020-07-14T01:56:04 prefetch.2.10.7: 1) Downloading 'SRR11978069'... 2020-07-14T01:56:04 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:56:38 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:56:38 prefetch.2.10.7: 'SRR11978069' is valid 2020-07-14T01:56:38 prefetch.2.10.7: 1) 'SRR11978069' was downloaded successfully 2020-07-14T01:56:39 prefetch.2.10.7: 'SRR11978069' has 0 unresolved dependencies Read 3281865 spots for SRR11978069/SRR11978069.sra Written 3281865 spots for SRR11978069/SRR11978069.sra 2020-07-14T01:57:03 prefetch.2.10.7: 1) Downloading 'SRR11978070'... 2020-07-14T01:57:03 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:58:34 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:58:35 prefetch.2.10.7: 'SRR11978070' is valid 2020-07-14T01:58:35 prefetch.2.10.7: 1) 'SRR11978070' was downloaded successfully 2020-07-14T01:58:35 prefetch.2.10.7: 'SRR11978070' has 0 unresolved dependencies Read 11722478 spots for SRR11978070/SRR11978070.sra Written 11722478 spots for SRR11978070/SRR11978070.sra 2020-07-14T01:59:28 prefetch.2.10.7: 1) Downloading 'SRR11978071'... 2020-07-14T01:59:28 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:00:35 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:00:36 prefetch.2.10.7: 'SRR11978071' is valid 2020-07-14T02:00:36 prefetch.2.10.7: 1) 'SRR11978071' was downloaded successfully 2020-07-14T02:00:36 prefetch.2.10.7: 'SRR11978071' has 0 unresolved dependencies Read 10864600 spots for SRR11978071/SRR11978071.sra Written 10864600 spots for SRR11978071/SRR11978071.sra 2020-07-14T02:01:26 prefetch.2.10.7: 1) Downloading 'SRR11978072'... 2020-07-14T02:01:26 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:04:25 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:04:26 prefetch.2.10.7: 'SRR11978072' is valid 2020-07-14T02:04:26 prefetch.2.10.7: 1) 'SRR11978072' was downloaded successfully 2020-07-14T02:04:26 prefetch.2.10.7: 'SRR11978072' has 0 unresolved dependencies Read 11358679 spots for SRR11978072/SRR11978072.sra Written 11358679 spots for SRR11978072/SRR11978072.sra 2020-07-14T02:05:14 prefetch.2.10.7: 1) Downloading 'SRR11978073'... 2020-07-14T02:05:14 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:06:41 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:06:42 prefetch.2.10.7: 'SRR11978073' is valid 2020-07-14T02:06:42 prefetch.2.10.7: 1) 'SRR11978073' was downloaded successfully 2020-07-14T02:06:42 prefetch.2.10.7: 'SRR11978073' has 0 unresolved dependencies Read 11393229 spots for SRR11978073/SRR11978073.sra Written 11393229 spots for SRR11978073/SRR11978073.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627551 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:00 58473180 reads; of these: 58473180 (100.00%) were unpaired; of these: 47136434 (80.61%) aligned 0 times 8578822 (14.67%) aligned exactly 1 time 2757924 (4.72%) aligned >1 times 19.39% overall alignment rate Time searching: 00:09:01 Overall time: 00:09:01 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] 2238949 / 11336746 = 0.1975 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 11:20:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.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 11:20:05: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:20:05: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:20:12: 1000000 INFO @ Tue, 14 Jul 2020 11:20:18: 2000000 INFO @ Tue, 14 Jul 2020 11:20:24: 3000000 INFO @ Tue, 14 Jul 2020 11:20:30: 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 11:20:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.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 11:20:35: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:20:35: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:20:36: 5000000 INFO @ Tue, 14 Jul 2020 11:20:42: 1000000 INFO @ Tue, 14 Jul 2020 11:20:43: 6000000 INFO @ Tue, 14 Jul 2020 11:20:48: 2000000 INFO @ Tue, 14 Jul 2020 11:20:49: 7000000 INFO @ Tue, 14 Jul 2020 11:20:54: 3000000 INFO @ Tue, 14 Jul 2020 11:20:56: 8000000 INFO @ Tue, 14 Jul 2020 11:21:01: 4000000 INFO @ Tue, 14 Jul 2020 11:21:02: 9000000 INFO @ Tue, 14 Jul 2020 11:21:03: #1 tag size is determined as 57 bps INFO @ Tue, 14 Jul 2020 11:21:03: #1 tag size = 57 INFO @ Tue, 14 Jul 2020 11:21:03: #1 total tags in treatment: 9097797 INFO @ Tue, 14 Jul 2020 11:21:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:21:03: #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 11:21:03: #1 tags after filtering in treatment: 9097797 INFO @ Tue, 14 Jul 2020 11:21:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:21:03: #1 finished! INFO @ Tue, 14 Jul 2020 11:21:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:21:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:21:03: #2 number of paired peaks: 236 WARNING @ Tue, 14 Jul 2020 11:21:03: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 14 Jul 2020 11:21:03: start model_add_line... 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 11:21:03: start X-correlation... INFO @ Tue, 14 Jul 2020 11:21:03: end of X-cor INFO @ Tue, 14 Jul 2020 11:21:03: #2 finished! INFO @ Tue, 14 Jul 2020 11:21:03: #2 predicted fragment length is 49 bps INFO @ Tue, 14 Jul 2020 11:21:03: #2 alternative fragment length(s) may be 44,49 bps INFO @ Tue, 14 Jul 2020 11:21:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.05_model.r WARNING @ Tue, 14 Jul 2020 11:21:03: #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 11:21:03: #2 You may need to consider one of the other alternative d(s): 44,49 WARNING @ Tue, 14 Jul 2020 11:21:03: #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 11:21:03: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:21:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:21:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.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 11:21:05: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:21:05: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:21:07: 5000000 INFO @ Tue, 14 Jul 2020 11:21:13: 6000000 INFO @ Tue, 14 Jul 2020 11:21:14: 1000000 INFO @ Tue, 14 Jul 2020 11:21:20: 7000000 INFO @ Tue, 14 Jul 2020 11:21:21: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:21:22: 2000000 INFO @ Tue, 14 Jul 2020 11:21:26: 8000000 INFO @ Tue, 14 Jul 2020 11:21:29: 3000000 INFO @ Tue, 14 Jul 2020 11:21:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:21:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:21:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.05_summits.bed INFO @ Tue, 14 Jul 2020 11:21:31: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2529 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:21:32: 9000000 INFO @ Tue, 14 Jul 2020 11:21:33: #1 tag size is determined as 57 bps INFO @ Tue, 14 Jul 2020 11:21:33: #1 tag size = 57 INFO @ Tue, 14 Jul 2020 11:21:33: #1 total tags in treatment: 9097797 INFO @ Tue, 14 Jul 2020 11:21:33: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:21:33: #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 11:21:33: #1 tags after filtering in treatment: 9097797 INFO @ Tue, 14 Jul 2020 11:21:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:21:33: #1 finished! INFO @ Tue, 14 Jul 2020 11:21:33: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:21:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:21:33: #2 number of paired peaks: 236 WARNING @ Tue, 14 Jul 2020 11:21:33: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 14 Jul 2020 11:21:33: start model_add_line... INFO @ Tue, 14 Jul 2020 11:21:33: start X-correlation... INFO @ Tue, 14 Jul 2020 11:21:34: end of X-cor INFO @ Tue, 14 Jul 2020 11:21:34: #2 finished! INFO @ Tue, 14 Jul 2020 11:21:34: #2 predicted fragment length is 49 bps INFO @ Tue, 14 Jul 2020 11:21:34: #2 alternative fragment length(s) may be 44,49 bps INFO @ Tue, 14 Jul 2020 11:21:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.10_model.r WARNING @ Tue, 14 Jul 2020 11:21:34: #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 11:21:34: #2 You may need to consider one of the other alternative d(s): 44,49 WARNING @ Tue, 14 Jul 2020 11:21:34: #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 11:21:34: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:21:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:21:37: 4000000 INFO @ Tue, 14 Jul 2020 11:21:45: 5000000 INFO @ Tue, 14 Jul 2020 11:21:51: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:21:53: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:22:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:22:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:22:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.10_summits.bed INFO @ Tue, 14 Jul 2020 11:22:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (971 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:22:01: 7000000 INFO @ Tue, 14 Jul 2020 11:22:09: 8000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:22:17: 9000000 INFO @ Tue, 14 Jul 2020 11:22:17: #1 tag size is determined as 57 bps INFO @ Tue, 14 Jul 2020 11:22:17: #1 tag size = 57 INFO @ Tue, 14 Jul 2020 11:22:17: #1 total tags in treatment: 9097797 INFO @ Tue, 14 Jul 2020 11:22:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:22:17: #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 11:22:18: #1 tags after filtering in treatment: 9097797 INFO @ Tue, 14 Jul 2020 11:22:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:22:18: #1 finished! INFO @ Tue, 14 Jul 2020 11:22:18: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:22:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:22:18: #2 number of paired peaks: 236 WARNING @ Tue, 14 Jul 2020 11:22:18: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 14 Jul 2020 11:22:18: start model_add_line... INFO @ Tue, 14 Jul 2020 11:22:18: start X-correlation... INFO @ Tue, 14 Jul 2020 11:22:18: end of X-cor INFO @ Tue, 14 Jul 2020 11:22:18: #2 finished! INFO @ Tue, 14 Jul 2020 11:22:18: #2 predicted fragment length is 49 bps INFO @ Tue, 14 Jul 2020 11:22:18: #2 alternative fragment length(s) may be 44,49 bps INFO @ Tue, 14 Jul 2020 11:22:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.20_model.r WARNING @ Tue, 14 Jul 2020 11:22:18: #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 11:22:18: #2 You may need to consider one of the other alternative d(s): 44,49 WARNING @ Tue, 14 Jul 2020 11:22:18: #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 11:22:18: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:22:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:22:37: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:22:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:22:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:22:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521355/SRX8521355.20_summits.bed INFO @ Tue, 14 Jul 2020 11:22:47: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (150 records, 4 fields): 1 millis CompletedMACS2peakCalling