Job ID = 6626768 SRX = SRX7780028 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-13T23:39:36 prefetch.2.10.7: 1) Downloading 'SRR11143783'... 2020-07-13T23:39:36 prefetch.2.10.7: Downloading via HTTPS... 2020-07-13T23:41:17 prefetch.2.10.7: HTTPS download succeed 2020-07-13T23:41:18 prefetch.2.10.7: 'SRR11143783' is valid 2020-07-13T23:41:18 prefetch.2.10.7: 1) 'SRR11143783' was downloaded successfully Read 13921082 spots for SRR11143783/SRR11143783.sra Written 13921082 spots for SRR11143783/SRR11143783.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627035 ("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: 00:04:40 13921082 reads; of these: 13921082 (100.00%) were unpaired; of these: 1725171 (12.39%) aligned 0 times 8432822 (60.58%) aligned exactly 1 time 3763089 (27.03%) aligned >1 times 87.61% overall alignment rate Time searching: 00:04:40 Overall time: 00:04:40 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] 1946084 / 12195911 = 0.1596 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 08:49:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.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 08:49:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:49:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:50:03: 1000000 INFO @ Tue, 14 Jul 2020 08:50:11: 2000000 INFO @ Tue, 14 Jul 2020 08:50:17: 3000000 INFO @ Tue, 14 Jul 2020 08:50:24: 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 08:50:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.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 08:50:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:50:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:50:31: 5000000 INFO @ Tue, 14 Jul 2020 08:50:35: 1000000 INFO @ Tue, 14 Jul 2020 08:50:38: 6000000 INFO @ Tue, 14 Jul 2020 08:50:45: 2000000 INFO @ Tue, 14 Jul 2020 08:50:45: 7000000 INFO @ Tue, 14 Jul 2020 08:50:52: 8000000 INFO @ Tue, 14 Jul 2020 08:50:54: 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 08:50:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.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 08:50:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:50:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:50:59: 9000000 INFO @ Tue, 14 Jul 2020 08:51:04: 4000000 INFO @ Tue, 14 Jul 2020 08:51:05: 1000000 INFO @ Tue, 14 Jul 2020 08:51:07: 10000000 INFO @ Tue, 14 Jul 2020 08:51:08: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 08:51:08: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 08:51:08: #1 total tags in treatment: 10249827 INFO @ Tue, 14 Jul 2020 08:51:08: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:51:08: #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 08:51:09: #1 tags after filtering in treatment: 10249827 INFO @ Tue, 14 Jul 2020 08:51:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:51:09: #1 finished! INFO @ Tue, 14 Jul 2020 08:51:09: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:51:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:51:09: #2 number of paired peaks: 143 WARNING @ Tue, 14 Jul 2020 08:51:09: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Tue, 14 Jul 2020 08:51:09: start model_add_line... INFO @ Tue, 14 Jul 2020 08:51:09: start X-correlation... INFO @ Tue, 14 Jul 2020 08:51:10: end of X-cor INFO @ Tue, 14 Jul 2020 08:51:10: #2 finished! INFO @ Tue, 14 Jul 2020 08:51:10: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 08:51:10: #2 alternative fragment length(s) may be 3,56,82,329,553 bps INFO @ Tue, 14 Jul 2020 08:51:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.05_model.r WARNING @ Tue, 14 Jul 2020 08:51:10: #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 08:51:10: #2 You may need to consider one of the other alternative d(s): 3,56,82,329,553 WARNING @ Tue, 14 Jul 2020 08:51:10: #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 08:51:10: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:51:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:51:13: 5000000 INFO @ Tue, 14 Jul 2020 08:51:14: 2000000 INFO @ Tue, 14 Jul 2020 08:51:22: 3000000 INFO @ Tue, 14 Jul 2020 08:51:22: 6000000 INFO @ Tue, 14 Jul 2020 08:51:29: 4000000 INFO @ Tue, 14 Jul 2020 08:51:31: 7000000 INFO @ Tue, 14 Jul 2020 08:51:32: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:51:36: 5000000 INFO @ Tue, 14 Jul 2020 08:51:40: 8000000 INFO @ Tue, 14 Jul 2020 08:51:43: 6000000 INFO @ Tue, 14 Jul 2020 08:51:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:51:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:51:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.05_summits.bed INFO @ Tue, 14 Jul 2020 08:51:44: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (454 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:51:49: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:51:50: 7000000 INFO @ Tue, 14 Jul 2020 08:51:57: 8000000 INFO @ Tue, 14 Jul 2020 08:51:58: 10000000 INFO @ Tue, 14 Jul 2020 08:52:00: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 08:52:00: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 08:52:00: #1 total tags in treatment: 10249827 INFO @ Tue, 14 Jul 2020 08:52:00: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:52:00: #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 08:52:01: #1 tags after filtering in treatment: 10249827 INFO @ Tue, 14 Jul 2020 08:52:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:52:01: #1 finished! INFO @ Tue, 14 Jul 2020 08:52:01: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:52:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:52:01: #2 number of paired peaks: 143 WARNING @ Tue, 14 Jul 2020 08:52:01: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Tue, 14 Jul 2020 08:52:01: start model_add_line... INFO @ Tue, 14 Jul 2020 08:52:01: start X-correlation... INFO @ Tue, 14 Jul 2020 08:52:01: end of X-cor INFO @ Tue, 14 Jul 2020 08:52:01: #2 finished! INFO @ Tue, 14 Jul 2020 08:52:01: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 08:52:01: #2 alternative fragment length(s) may be 3,56,82,329,553 bps INFO @ Tue, 14 Jul 2020 08:52:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.10_model.r WARNING @ Tue, 14 Jul 2020 08:52:01: #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 08:52:01: #2 You may need to consider one of the other alternative d(s): 3,56,82,329,553 WARNING @ Tue, 14 Jul 2020 08:52:01: #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 08:52:01: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:52:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:52:04: 9000000 INFO @ Tue, 14 Jul 2020 08:52:12: 10000000 INFO @ Tue, 14 Jul 2020 08:52:13: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 08:52:13: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 08:52:13: #1 total tags in treatment: 10249827 INFO @ Tue, 14 Jul 2020 08:52:13: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:52:13: #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 08:52:13: #1 tags after filtering in treatment: 10249827 INFO @ Tue, 14 Jul 2020 08:52:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:52:13: #1 finished! INFO @ Tue, 14 Jul 2020 08:52:13: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:52:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:52:14: #2 number of paired peaks: 143 WARNING @ Tue, 14 Jul 2020 08:52:14: Fewer paired peaks (143) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 143 pairs to build model! INFO @ Tue, 14 Jul 2020 08:52:14: start model_add_line... INFO @ Tue, 14 Jul 2020 08:52:14: start X-correlation... INFO @ Tue, 14 Jul 2020 08:52:14: end of X-cor INFO @ Tue, 14 Jul 2020 08:52:14: #2 finished! INFO @ Tue, 14 Jul 2020 08:52:14: #2 predicted fragment length is 56 bps INFO @ Tue, 14 Jul 2020 08:52:14: #2 alternative fragment length(s) may be 3,56,82,329,553 bps INFO @ Tue, 14 Jul 2020 08:52:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.20_model.r WARNING @ Tue, 14 Jul 2020 08:52:14: #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 08:52:14: #2 You may need to consider one of the other alternative d(s): 3,56,82,329,553 WARNING @ Tue, 14 Jul 2020 08:52:14: #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 08:52:14: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:52:14: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:52:25: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:52:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:52:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:52:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.10_summits.bed INFO @ Tue, 14 Jul 2020 08:52:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (188 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:52:37: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:52:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:52:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:52:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7780028/SRX7780028.20_summits.bed INFO @ Tue, 14 Jul 2020 08:52:49: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (54 records, 4 fields): 1 millis CompletedMACS2peakCalling