Job ID = 6627146 SRX = SRX8521295 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:15:09 prefetch.2.10.7: 1) Downloading 'SRR11978474'... 2020-07-14T01:15:09 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:17:01 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:17:02 prefetch.2.10.7: 'SRR11978474' is valid 2020-07-14T01:17:02 prefetch.2.10.7: 1) 'SRR11978474' was downloaded successfully 2020-07-14T01:17:02 prefetch.2.10.7: 'SRR11978474' has 0 unresolved dependencies Read 11090473 spots for SRR11978474/SRR11978474.sra Written 11090473 spots for SRR11978474/SRR11978474.sra 2020-07-14T01:17:58 prefetch.2.10.7: 1) Downloading 'SRR11978475'... 2020-07-14T01:17:58 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:19:17 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:19:17 prefetch.2.10.7: 'SRR11978475' is valid 2020-07-14T01:19:17 prefetch.2.10.7: 1) 'SRR11978475' was downloaded successfully 2020-07-14T01:19:17 prefetch.2.10.7: 'SRR11978475' has 0 unresolved dependencies Read 10156498 spots for SRR11978475/SRR11978475.sra Written 10156498 spots for SRR11978475/SRR11978475.sra 2020-07-14T01:20:07 prefetch.2.10.7: 1) Downloading 'SRR11978476'... 2020-07-14T01:20:07 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:22:09 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:22:10 prefetch.2.10.7: 'SRR11978476' is valid 2020-07-14T01:22:10 prefetch.2.10.7: 1) 'SRR11978476' was downloaded successfully 2020-07-14T01:22:10 prefetch.2.10.7: 'SRR11978476' has 0 unresolved dependencies Read 11068831 spots for SRR11978476/SRR11978476.sra Written 11068831 spots for SRR11978476/SRR11978476.sra 2020-07-14T01:23:06 prefetch.2.10.7: 1) Downloading 'SRR11978477'... 2020-07-14T01:23:06 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:24:19 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:24:20 prefetch.2.10.7: 'SRR11978477' is valid 2020-07-14T01:24:20 prefetch.2.10.7: 1) 'SRR11978477' was downloaded successfully 2020-07-14T01:24:20 prefetch.2.10.7: 'SRR11978477' has 0 unresolved dependencies Read 11472499 spots for SRR11978477/SRR11978477.sra Written 11472499 spots for SRR11978477/SRR11978477.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627412 ("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: 00:11:03 43788301 reads; of these: 43788301 (100.00%) were unpaired; of these: 34651184 (79.13%) aligned 0 times 5244672 (11.98%) aligned exactly 1 time 3892445 (8.89%) aligned >1 times 20.87% overall alignment rate Time searching: 00:11:03 Overall time: 00:11:03 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] 2670484 / 9137117 = 0.2923 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 10:39:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.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 10:39:52: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:39:52: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:39:59: 1000000 INFO @ Tue, 14 Jul 2020 10:40:05: 2000000 INFO @ Tue, 14 Jul 2020 10:40:12: 3000000 INFO @ Tue, 14 Jul 2020 10:40:19: 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 10:40:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.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 10:40:22: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:40:22: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:40:26: 5000000 INFO @ Tue, 14 Jul 2020 10:40:29: 1000000 INFO @ Tue, 14 Jul 2020 10:40:33: 6000000 INFO @ Tue, 14 Jul 2020 10:40:36: #1 tag size is determined as 70 bps INFO @ Tue, 14 Jul 2020 10:40:36: #1 tag size = 70 INFO @ Tue, 14 Jul 2020 10:40:36: #1 total tags in treatment: 6466633 INFO @ Tue, 14 Jul 2020 10:40:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:40:36: #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 10:40:37: #1 tags after filtering in treatment: 6466633 INFO @ Tue, 14 Jul 2020 10:40:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:40:37: #1 finished! INFO @ Tue, 14 Jul 2020 10:40:37: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:40:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:40:37: 2000000 INFO @ Tue, 14 Jul 2020 10:40:37: #2 number of paired peaks: 362 WARNING @ Tue, 14 Jul 2020 10:40:37: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Tue, 14 Jul 2020 10:40:37: start model_add_line... INFO @ Tue, 14 Jul 2020 10:40:37: start X-correlation... INFO @ Tue, 14 Jul 2020 10:40:37: end of X-cor INFO @ Tue, 14 Jul 2020 10:40:37: #2 finished! INFO @ Tue, 14 Jul 2020 10:40:37: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 10:40:37: #2 alternative fragment length(s) may be 56 bps INFO @ Tue, 14 Jul 2020 10:40:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.05_model.r WARNING @ Tue, 14 Jul 2020 10:40:37: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:40:37: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Tue, 14 Jul 2020 10:40:37: #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 10:40:37: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:40:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:40:44: 3000000 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 10:40:51: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:40:51: 4000000 INFO @ Tue, 14 Jul 2020 10:40:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.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 10:40:52: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:40:52: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:40:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:40:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:40:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.05_summits.bed INFO @ Tue, 14 Jul 2020 10:40:58: Done! INFO @ Tue, 14 Jul 2020 10:40:58: 5000000 INFO @ Tue, 14 Jul 2020 10:40:59: 1000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1853 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:41:05: 6000000 INFO @ Tue, 14 Jul 2020 10:41:07: 2000000 INFO @ Tue, 14 Jul 2020 10:41:08: #1 tag size is determined as 70 bps INFO @ Tue, 14 Jul 2020 10:41:08: #1 tag size = 70 INFO @ Tue, 14 Jul 2020 10:41:08: #1 total tags in treatment: 6466633 INFO @ Tue, 14 Jul 2020 10:41:08: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:41:08: #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 10:41:08: #1 tags after filtering in treatment: 6466633 INFO @ Tue, 14 Jul 2020 10:41:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:41:08: #1 finished! INFO @ Tue, 14 Jul 2020 10:41:08: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:41:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:41:09: #2 number of paired peaks: 362 WARNING @ Tue, 14 Jul 2020 10:41:09: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Tue, 14 Jul 2020 10:41:09: start model_add_line... INFO @ Tue, 14 Jul 2020 10:41:09: start X-correlation... INFO @ Tue, 14 Jul 2020 10:41:09: end of X-cor INFO @ Tue, 14 Jul 2020 10:41:09: #2 finished! INFO @ Tue, 14 Jul 2020 10:41:09: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 10:41:09: #2 alternative fragment length(s) may be 56 bps INFO @ Tue, 14 Jul 2020 10:41:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.10_model.r WARNING @ Tue, 14 Jul 2020 10:41:09: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:41:09: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Tue, 14 Jul 2020 10:41:09: #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 10:41:09: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:41:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:41:13: 3000000 INFO @ Tue, 14 Jul 2020 10:41:20: 4000000 INFO @ Tue, 14 Jul 2020 10:41:22: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:41:26: 5000000 INFO @ Tue, 14 Jul 2020 10:41:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:41:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:41:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.10_summits.bed INFO @ Tue, 14 Jul 2020 10:41:29: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (929 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:41:33: 6000000 INFO @ Tue, 14 Jul 2020 10:41:35: #1 tag size is determined as 70 bps INFO @ Tue, 14 Jul 2020 10:41:35: #1 tag size = 70 INFO @ Tue, 14 Jul 2020 10:41:35: #1 total tags in treatment: 6466633 INFO @ Tue, 14 Jul 2020 10:41:35: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:41:35: #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 10:41:36: #1 tags after filtering in treatment: 6466633 INFO @ Tue, 14 Jul 2020 10:41:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:41:36: #1 finished! INFO @ Tue, 14 Jul 2020 10:41:36: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:41:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:41:36: #2 number of paired peaks: 362 WARNING @ Tue, 14 Jul 2020 10:41:36: Fewer paired peaks (362) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 362 pairs to build model! INFO @ Tue, 14 Jul 2020 10:41:36: start model_add_line... INFO @ Tue, 14 Jul 2020 10:41:36: start X-correlation... INFO @ Tue, 14 Jul 2020 10:41:36: end of X-cor INFO @ Tue, 14 Jul 2020 10:41:36: #2 finished! INFO @ Tue, 14 Jul 2020 10:41:36: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 10:41:36: #2 alternative fragment length(s) may be 56 bps INFO @ Tue, 14 Jul 2020 10:41:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.20_model.r WARNING @ Tue, 14 Jul 2020 10:41:36: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:41:36: #2 You may need to consider one of the other alternative d(s): 56 WARNING @ Tue, 14 Jul 2020 10:41:36: #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 10:41:36: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:41:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:41:49: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:41:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:41:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:41:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521295/SRX8521295.20_summits.bed INFO @ Tue, 14 Jul 2020 10:41:56: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (367 records, 4 fields): 2 millis CompletedMACS2peakCalling