Job ID = 6627258 SRX = SRX8521330 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:40:50 prefetch.2.10.7: 1) Downloading 'SRR11977989'... 2020-07-14T01:40:50 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:42:01 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:42:01 prefetch.2.10.7: 'SRR11977989' is valid 2020-07-14T01:42:01 prefetch.2.10.7: 1) 'SRR11977989' was downloaded successfully 2020-07-14T01:42:01 prefetch.2.10.7: 'SRR11977989' has 0 unresolved dependencies Read 10245342 spots for SRR11977989/SRR11977989.sra Written 10245342 spots for SRR11977989/SRR11977989.sra 2020-07-14T01:42:47 prefetch.2.10.7: 1) Downloading 'SRR11977990'... 2020-07-14T01:42:47 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:44:06 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:44:07 prefetch.2.10.7: 'SRR11977990' is valid 2020-07-14T01:44:07 prefetch.2.10.7: 1) 'SRR11977990' was downloaded successfully 2020-07-14T01:44:07 prefetch.2.10.7: 'SRR11977990' has 0 unresolved dependencies Read 10011908 spots for SRR11977990/SRR11977990.sra Written 10011908 spots for SRR11977990/SRR11977990.sra 2020-07-14T01:44:51 prefetch.2.10.7: 1) Downloading 'SRR11977991'... 2020-07-14T01:44:51 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:46:12 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:46:13 prefetch.2.10.7: 'SRR11977991' is valid 2020-07-14T01:46:13 prefetch.2.10.7: 1) 'SRR11977991' was downloaded successfully 2020-07-14T01:46:13 prefetch.2.10.7: 'SRR11977991' has 0 unresolved dependencies Read 10200724 spots for SRR11977991/SRR11977991.sra Written 10200724 spots for SRR11977991/SRR11977991.sra 2020-07-14T01:46:57 prefetch.2.10.7: 1) Downloading 'SRR11977992'... 2020-07-14T01:46:57 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:48:21 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:48:22 prefetch.2.10.7: 'SRR11977992' is valid 2020-07-14T01:48:22 prefetch.2.10.7: 1) 'SRR11977992' was downloaded successfully 2020-07-14T01:48:22 prefetch.2.10.7: 'SRR11977992' has 0 unresolved dependencies Read 10461614 spots for SRR11977992/SRR11977992.sra Written 10461614 spots for SRR11977992/SRR11977992.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627463 ("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: 00:05:39 40919588 reads; of these: 40919588 (100.00%) were unpaired; of these: 35236819 (86.11%) aligned 0 times 4414246 (10.79%) aligned exactly 1 time 1268523 (3.10%) aligned >1 times 13.89% overall alignment rate Time searching: 00:05:39 Overall time: 00:05:39 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] 982979 / 5682769 = 0.1730 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 10:56:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.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 10:56:51: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:56:51: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:56:57: 1000000 INFO @ Tue, 14 Jul 2020 10:57:03: 2000000 INFO @ Tue, 14 Jul 2020 10:57:08: 3000000 INFO @ Tue, 14 Jul 2020 10:57:13: 4000000 INFO @ Tue, 14 Jul 2020 10:57:17: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 10:57:17: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 10:57:17: #1 total tags in treatment: 4699790 INFO @ Tue, 14 Jul 2020 10:57:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:57:17: #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 10:57:17: #1 tags after filtering in treatment: 4699790 INFO @ Tue, 14 Jul 2020 10:57:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:57:17: #1 finished! INFO @ Tue, 14 Jul 2020 10:57:17: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:57:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:57:17: #2 number of paired peaks: 508 WARNING @ Tue, 14 Jul 2020 10:57:17: Fewer paired peaks (508) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 508 pairs to build model! INFO @ Tue, 14 Jul 2020 10:57:17: start model_add_line... INFO @ Tue, 14 Jul 2020 10:57:17: start X-correlation... INFO @ Tue, 14 Jul 2020 10:57:17: end of X-cor INFO @ Tue, 14 Jul 2020 10:57:17: #2 finished! INFO @ Tue, 14 Jul 2020 10:57:17: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 10:57:17: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 10:57:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.05_model.r WARNING @ Tue, 14 Jul 2020 10:57:17: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:57:17: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 10:57:17: #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 10:57:17: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:57:17: #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 10:57:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.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 10:57:21: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:57:21: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:57:27: 1000000 INFO @ Tue, 14 Jul 2020 10:57:27: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:57:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:57:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:57:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.05_summits.bed INFO @ Tue, 14 Jul 2020 10:57:32: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1739 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:57:33: 2000000 INFO @ Tue, 14 Jul 2020 10:57:38: 3000000 INFO @ Tue, 14 Jul 2020 10:57:44: 4000000 INFO @ Tue, 14 Jul 2020 10:57:48: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 10:57:48: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 10:57:48: #1 total tags in treatment: 4699790 INFO @ Tue, 14 Jul 2020 10:57:48: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:57:48: #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 10:57:48: #1 tags after filtering in treatment: 4699790 INFO @ Tue, 14 Jul 2020 10:57:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:57:48: #1 finished! INFO @ Tue, 14 Jul 2020 10:57:48: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:57:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:57:49: #2 number of paired peaks: 508 WARNING @ Tue, 14 Jul 2020 10:57:49: Fewer paired peaks (508) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 508 pairs to build model! INFO @ Tue, 14 Jul 2020 10:57:49: start model_add_line... INFO @ Tue, 14 Jul 2020 10:57:49: start X-correlation... INFO @ Tue, 14 Jul 2020 10:57:49: end of X-cor INFO @ Tue, 14 Jul 2020 10:57:49: #2 finished! INFO @ Tue, 14 Jul 2020 10:57:49: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 10:57:49: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 10:57:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.10_model.r WARNING @ Tue, 14 Jul 2020 10:57:49: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:57:49: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 10:57:49: #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 10:57:49: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:57:49: #3 Pre-compute pvalue-qvalue table... 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 10:57:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.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 10:57:51: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:57:51: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:57:57: 1000000 INFO @ Tue, 14 Jul 2020 10:57:58: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:58:03: 2000000 INFO @ Tue, 14 Jul 2020 10:58:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:58:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:58:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.10_summits.bed INFO @ Tue, 14 Jul 2020 10:58:04: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (746 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:58:08: 3000000 INFO @ Tue, 14 Jul 2020 10:58:14: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:58:18: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 10:58:18: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 10:58:18: #1 total tags in treatment: 4699790 INFO @ Tue, 14 Jul 2020 10:58:18: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:58:18: #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 10:58:18: #1 tags after filtering in treatment: 4699790 INFO @ Tue, 14 Jul 2020 10:58:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:58:18: #1 finished! INFO @ Tue, 14 Jul 2020 10:58:18: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:58:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:58:19: #2 number of paired peaks: 508 WARNING @ Tue, 14 Jul 2020 10:58:19: Fewer paired peaks (508) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 508 pairs to build model! INFO @ Tue, 14 Jul 2020 10:58:19: start model_add_line... INFO @ Tue, 14 Jul 2020 10:58:19: start X-correlation... INFO @ Tue, 14 Jul 2020 10:58:19: end of X-cor INFO @ Tue, 14 Jul 2020 10:58:19: #2 finished! INFO @ Tue, 14 Jul 2020 10:58:19: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 10:58:19: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 10:58:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.20_model.r WARNING @ Tue, 14 Jul 2020 10:58:19: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:58:19: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 10:58:19: #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 10:58:19: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:58:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:58:29: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:58:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:58:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:58:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521330/SRX8521330.20_summits.bed INFO @ Tue, 14 Jul 2020 10:58:34: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (133 records, 4 fields): 1 millis CompletedMACS2peakCalling