Job ID = 6627473 SRX = SRX8521390 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T02:43:37 prefetch.2.10.7: 1) Downloading 'SRR11978302'... 2020-07-14T02:43:37 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:46:24 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:46:24 prefetch.2.10.7: 'SRR11978302' is valid 2020-07-14T02:46:24 prefetch.2.10.7: 1) 'SRR11978302' was downloaded successfully 2020-07-14T02:46:24 prefetch.2.10.7: 'SRR11978302' has 0 unresolved dependencies Read 13253363 spots for SRR11978302/SRR11978302.sra Written 13253363 spots for SRR11978302/SRR11978302.sra 2020-07-14T02:47:28 prefetch.2.10.7: 1) Downloading 'SRR11978303'... 2020-07-14T02:47:28 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:49:48 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:49:49 prefetch.2.10.7: 'SRR11978303' is valid 2020-07-14T02:49:49 prefetch.2.10.7: 1) 'SRR11978303' was downloaded successfully 2020-07-14T02:49:49 prefetch.2.10.7: 'SRR11978303' has 0 unresolved dependencies Read 13189587 spots for SRR11978303/SRR11978303.sra Written 13189587 spots for SRR11978303/SRR11978303.sra 2020-07-14T02:50:47 prefetch.2.10.7: 1) Downloading 'SRR11978304'... 2020-07-14T02:50:47 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:52:42 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:52:43 prefetch.2.10.7: 'SRR11978304' is valid 2020-07-14T02:52:43 prefetch.2.10.7: 1) 'SRR11978304' was downloaded successfully 2020-07-14T02:52:43 prefetch.2.10.7: 'SRR11978304' has 0 unresolved dependencies Read 13166293 spots for SRR11978304/SRR11978304.sra Written 13166293 spots for SRR11978304/SRR11978304.sra 2020-07-14T02:53:41 prefetch.2.10.7: 1) Downloading 'SRR11978305'... 2020-07-14T02:53:41 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:54:53 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:54:53 prefetch.2.10.7: 'SRR11978305' is valid 2020-07-14T02:54:53 prefetch.2.10.7: 1) 'SRR11978305' was downloaded successfully 2020-07-14T02:54:53 prefetch.2.10.7: 'SRR11978305' has 0 unresolved dependencies Read 13277212 spots for SRR11978305/SRR11978305.sra Written 13277212 spots for SRR11978305/SRR11978305.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627694 ("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: 00:06:49 52886455 reads; of these: 52886455 (100.00%) were unpaired; of these: 48793402 (92.26%) aligned 0 times 3046708 (5.76%) aligned exactly 1 time 1046345 (1.98%) aligned >1 times 7.74% overall alignment rate Time searching: 00:06:49 Overall time: 00:06:49 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] 795828 / 4093053 = 0.1944 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 12:04:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.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 12:04:19: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:04:19: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:04:24: 1000000 INFO @ Tue, 14 Jul 2020 12:04:29: 2000000 INFO @ Tue, 14 Jul 2020 12:04:35: 3000000 INFO @ Tue, 14 Jul 2020 12:04:36: #1 tag size is determined as 69 bps INFO @ Tue, 14 Jul 2020 12:04:36: #1 tag size = 69 INFO @ Tue, 14 Jul 2020 12:04:36: #1 total tags in treatment: 3297225 INFO @ Tue, 14 Jul 2020 12:04:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:04:36: #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 12:04:36: #1 tags after filtering in treatment: 3297225 INFO @ Tue, 14 Jul 2020 12:04:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:04:36: #1 finished! INFO @ Tue, 14 Jul 2020 12:04:36: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:04:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:04:36: #2 number of paired peaks: 670 WARNING @ Tue, 14 Jul 2020 12:04:36: Fewer paired peaks (670) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 670 pairs to build model! INFO @ Tue, 14 Jul 2020 12:04:36: start model_add_line... INFO @ Tue, 14 Jul 2020 12:04:36: start X-correlation... INFO @ Tue, 14 Jul 2020 12:04:36: end of X-cor INFO @ Tue, 14 Jul 2020 12:04:36: #2 finished! INFO @ Tue, 14 Jul 2020 12:04:36: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 12:04:36: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 12:04:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.05_model.r WARNING @ Tue, 14 Jul 2020 12:04:37: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:04:37: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 12:04:37: #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 12:04:37: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:04:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:04:44: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:04:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:04:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:04:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.05_summits.bed INFO @ Tue, 14 Jul 2020 12:04:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1438 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 12:04:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.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 12:04:49: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:04:49: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:04:54: 1000000 INFO @ Tue, 14 Jul 2020 12:05:00: 2000000 INFO @ Tue, 14 Jul 2020 12:05:05: 3000000 INFO @ Tue, 14 Jul 2020 12:05:06: #1 tag size is determined as 69 bps INFO @ Tue, 14 Jul 2020 12:05:06: #1 tag size = 69 INFO @ Tue, 14 Jul 2020 12:05:06: #1 total tags in treatment: 3297225 INFO @ Tue, 14 Jul 2020 12:05:06: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:05:06: #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 12:05:06: #1 tags after filtering in treatment: 3297225 INFO @ Tue, 14 Jul 2020 12:05:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:05:06: #1 finished! INFO @ Tue, 14 Jul 2020 12:05:06: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:05:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:05:07: #2 number of paired peaks: 670 WARNING @ Tue, 14 Jul 2020 12:05:07: Fewer paired peaks (670) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 670 pairs to build model! INFO @ Tue, 14 Jul 2020 12:05:07: start model_add_line... INFO @ Tue, 14 Jul 2020 12:05:07: start X-correlation... INFO @ Tue, 14 Jul 2020 12:05:07: end of X-cor INFO @ Tue, 14 Jul 2020 12:05:07: #2 finished! INFO @ Tue, 14 Jul 2020 12:05:07: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 12:05:07: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 12:05:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.10_model.r WARNING @ Tue, 14 Jul 2020 12:05:07: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:05:07: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 12:05:07: #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 12:05:07: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:05:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:05:14: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:05:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:05:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:05:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.10_summits.bed INFO @ Tue, 14 Jul 2020 12:05:17: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (647 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 12:05:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.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 12:05:19: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:05:19: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:05:25: 1000000 INFO @ Tue, 14 Jul 2020 12:05:30: 2000000 INFO @ Tue, 14 Jul 2020 12:05:36: 3000000 INFO @ Tue, 14 Jul 2020 12:05:37: #1 tag size is determined as 69 bps INFO @ Tue, 14 Jul 2020 12:05:37: #1 tag size = 69 INFO @ Tue, 14 Jul 2020 12:05:37: #1 total tags in treatment: 3297225 INFO @ Tue, 14 Jul 2020 12:05:37: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:05:37: #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 12:05:37: #1 tags after filtering in treatment: 3297225 INFO @ Tue, 14 Jul 2020 12:05:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:05:37: #1 finished! INFO @ Tue, 14 Jul 2020 12:05:37: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:05:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:05:38: #2 number of paired peaks: 670 WARNING @ Tue, 14 Jul 2020 12:05:38: Fewer paired peaks (670) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 670 pairs to build model! INFO @ Tue, 14 Jul 2020 12:05:38: start model_add_line... INFO @ Tue, 14 Jul 2020 12:05:38: start X-correlation... INFO @ Tue, 14 Jul 2020 12:05:38: end of X-cor INFO @ Tue, 14 Jul 2020 12:05:38: #2 finished! INFO @ Tue, 14 Jul 2020 12:05:38: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 12:05:38: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 12:05:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.20_model.r WARNING @ Tue, 14 Jul 2020 12:05:38: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:05:38: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 12:05:38: #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 12:05:38: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:05:38: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:05:45: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:05:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:05:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:05:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521390/SRX8521390.20_summits.bed INFO @ Tue, 14 Jul 2020 12:05:49: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (160 records, 4 fields): 1 millis CompletedMACS2peakCalling