Job ID = 6627560 SRX = SRX8521399 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T02:58:51 prefetch.2.10.7: 1) Downloading 'SRR11978338'... 2020-07-14T02:58:51 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:05:14 prefetch.2.10.7: HTTPS download failed 2020-07-14T03:05:14 prefetch.2.10.7: 1) failed to download SRR11978338 2020-07-14T03:06:10 prefetch.2.10.7: 1) Downloading 'SRR11978338'... 2020-07-14T03:06:10 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:06:10 prefetch.2.10.7: Continue download of 'SRR11978338' from 326552207 2020-07-14T03:06:33 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:06:33 prefetch.2.10.7: 'SRR11978338' is valid 2020-07-14T03:06:33 prefetch.2.10.7: 1) 'SRR11978338' was downloaded successfully 2020-07-14T03:06:33 prefetch.2.10.7: 'SRR11978338' has 0 unresolved dependencies Read 12281317 spots for SRR11978338/SRR11978338.sra Written 12281317 spots for SRR11978338/SRR11978338.sra 2020-07-14T03:07:28 prefetch.2.10.7: 1) Downloading 'SRR11978339'... 2020-07-14T03:07:28 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:08:52 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:08:52 prefetch.2.10.7: 'SRR11978339' is valid 2020-07-14T03:08:52 prefetch.2.10.7: 1) 'SRR11978339' was downloaded successfully 2020-07-14T03:08:52 prefetch.2.10.7: 'SRR11978339' has 0 unresolved dependencies Read 12282028 spots for SRR11978339/SRR11978339.sra Written 12282028 spots for SRR11978339/SRR11978339.sra 2020-07-14T03:09:43 prefetch.2.10.7: 1) Downloading 'SRR11978340'... 2020-07-14T03:09:43 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:11:41 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:11:41 prefetch.2.10.7: 'SRR11978340' is valid 2020-07-14T03:11:41 prefetch.2.10.7: 1) 'SRR11978340' was downloaded successfully 2020-07-14T03:11:41 prefetch.2.10.7: 'SRR11978340' has 0 unresolved dependencies Read 12472476 spots for SRR11978340/SRR11978340.sra Written 12472476 spots for SRR11978340/SRR11978340.sra 2020-07-14T03:12:44 prefetch.2.10.7: 1) Downloading 'SRR11978341'... 2020-07-14T03:12:44 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:14:02 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:14:02 prefetch.2.10.7: 'SRR11978341' is valid 2020-07-14T03:14:02 prefetch.2.10.7: 1) 'SRR11978341' was downloaded successfully 2020-07-14T03:14:02 prefetch.2.10.7: 'SRR11978341' has 0 unresolved dependencies Read 12372676 spots for SRR11978341/SRR11978341.sra Written 12372676 spots for SRR11978341/SRR11978341.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627773 ("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: 00:08:36 49408497 reads; of these: 49408497 (100.00%) were unpaired; of these: 38598898 (78.12%) aligned 0 times 7977786 (16.15%) aligned exactly 1 time 2831813 (5.73%) aligned >1 times 21.88% overall alignment rate Time searching: 00:08:36 Overall time: 00:08:36 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] 1887786 / 10809599 = 0.1746 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 12:26:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.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 12:26:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:26:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:27:01: 1000000 INFO @ Tue, 14 Jul 2020 12:27:05: 2000000 INFO @ Tue, 14 Jul 2020 12:27:10: 3000000 INFO @ Tue, 14 Jul 2020 12:27:15: 4000000 INFO @ Tue, 14 Jul 2020 12:27:20: 5000000 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 12:27:25: 6000000 INFO @ Tue, 14 Jul 2020 12:27:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.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 12:27:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:27:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:27:30: 7000000 INFO @ Tue, 14 Jul 2020 12:27:32: 1000000 INFO @ Tue, 14 Jul 2020 12:27:35: 8000000 INFO @ Tue, 14 Jul 2020 12:27:37: 2000000 INFO @ Tue, 14 Jul 2020 12:27:40: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:27:40: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:27:40: #1 total tags in treatment: 8921813 INFO @ Tue, 14 Jul 2020 12:27:40: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:27:40: #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 12:27:40: #1 tags after filtering in treatment: 8921813 INFO @ Tue, 14 Jul 2020 12:27:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:27:40: #1 finished! INFO @ Tue, 14 Jul 2020 12:27:40: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:27:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:27:40: #2 number of paired peaks: 227 WARNING @ Tue, 14 Jul 2020 12:27:40: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Tue, 14 Jul 2020 12:27:40: start model_add_line... INFO @ Tue, 14 Jul 2020 12:27:40: start X-correlation... INFO @ Tue, 14 Jul 2020 12:27:40: end of X-cor INFO @ Tue, 14 Jul 2020 12:27:40: #2 finished! INFO @ Tue, 14 Jul 2020 12:27:40: #2 predicted fragment length is 52 bps INFO @ Tue, 14 Jul 2020 12:27:40: #2 alternative fragment length(s) may be 52 bps INFO @ Tue, 14 Jul 2020 12:27:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.05_model.r WARNING @ Tue, 14 Jul 2020 12:27:40: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:27:40: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Tue, 14 Jul 2020 12:27:40: #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 12:27:40: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:27:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:27:42: 3000000 INFO @ Tue, 14 Jul 2020 12:27:47: 4000000 INFO @ Tue, 14 Jul 2020 12:27:52: 5000000 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 12:27:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.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 12:27:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:27:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:27:57: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:27:58: 6000000 INFO @ Tue, 14 Jul 2020 12:28:02: 1000000 INFO @ Tue, 14 Jul 2020 12:28:03: 7000000 INFO @ Tue, 14 Jul 2020 12:28:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:28:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:28:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.05_summits.bed INFO @ Tue, 14 Jul 2020 12:28:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2228 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:28:08: 2000000 INFO @ Tue, 14 Jul 2020 12:28:09: 8000000 INFO @ Tue, 14 Jul 2020 12:28:14: 3000000 INFO @ Tue, 14 Jul 2020 12:28:15: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:28:15: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:28:15: #1 total tags in treatment: 8921813 INFO @ Tue, 14 Jul 2020 12:28:15: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:28:15: #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 12:28:15: #1 tags after filtering in treatment: 8921813 INFO @ Tue, 14 Jul 2020 12:28:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:28:15: #1 finished! INFO @ Tue, 14 Jul 2020 12:28:15: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:28:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:28:15: #2 number of paired peaks: 227 WARNING @ Tue, 14 Jul 2020 12:28:15: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Tue, 14 Jul 2020 12:28:15: start model_add_line... INFO @ Tue, 14 Jul 2020 12:28:16: start X-correlation... INFO @ Tue, 14 Jul 2020 12:28:16: end of X-cor INFO @ Tue, 14 Jul 2020 12:28:16: #2 finished! INFO @ Tue, 14 Jul 2020 12:28:16: #2 predicted fragment length is 52 bps INFO @ Tue, 14 Jul 2020 12:28:16: #2 alternative fragment length(s) may be 52 bps INFO @ Tue, 14 Jul 2020 12:28:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.10_model.r WARNING @ Tue, 14 Jul 2020 12:28:16: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:28:16: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Tue, 14 Jul 2020 12:28:16: #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 12:28:16: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:28:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:28:20: 4000000 INFO @ Tue, 14 Jul 2020 12:28:25: 5000000 INFO @ Tue, 14 Jul 2020 12:28:30: 6000000 INFO @ Tue, 14 Jul 2020 12:28:33: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:28:35: 7000000 INFO @ Tue, 14 Jul 2020 12:28:41: 8000000 INFO @ Tue, 14 Jul 2020 12:28:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:28:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:28:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.10_summits.bed INFO @ Tue, 14 Jul 2020 12:28:43: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (942 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:28:45: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:28:45: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:28:45: #1 total tags in treatment: 8921813 INFO @ Tue, 14 Jul 2020 12:28:45: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:28:45: #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 12:28:45: #1 tags after filtering in treatment: 8921813 INFO @ Tue, 14 Jul 2020 12:28:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:28:45: #1 finished! INFO @ Tue, 14 Jul 2020 12:28:45: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:28:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:28:46: #2 number of paired peaks: 227 WARNING @ Tue, 14 Jul 2020 12:28:46: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Tue, 14 Jul 2020 12:28:46: start model_add_line... INFO @ Tue, 14 Jul 2020 12:28:46: start X-correlation... INFO @ Tue, 14 Jul 2020 12:28:46: end of X-cor INFO @ Tue, 14 Jul 2020 12:28:46: #2 finished! INFO @ Tue, 14 Jul 2020 12:28:46: #2 predicted fragment length is 52 bps INFO @ Tue, 14 Jul 2020 12:28:46: #2 alternative fragment length(s) may be 52 bps INFO @ Tue, 14 Jul 2020 12:28:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.20_model.r WARNING @ Tue, 14 Jul 2020 12:28:46: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:28:46: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Tue, 14 Jul 2020 12:28:46: #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 12:28:46: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:28:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:29:04: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:29:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:29:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:29:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521399/SRX8521399.20_summits.bed INFO @ Tue, 14 Jul 2020 12:29:13: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (259 records, 4 fields): 2 millis CompletedMACS2peakCalling