Job ID = 6627164 SRX = SRX8521302 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:24:01 prefetch.2.10.7: 1) Downloading 'SRR11978530'... 2020-07-14T01:24:01 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:25:19 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:25:20 prefetch.2.10.7: 'SRR11978530' is valid 2020-07-14T01:25:20 prefetch.2.10.7: 1) 'SRR11978530' was downloaded successfully 2020-07-14T01:25:20 prefetch.2.10.7: 'SRR11978530' has 0 unresolved dependencies Read 9746510 spots for SRR11978530/SRR11978530.sra Written 9746510 spots for SRR11978530/SRR11978530.sra 2020-07-14T01:26:09 prefetch.2.10.7: 1) Downloading 'SRR11978531'... 2020-07-14T01:26:09 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:27:14 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:27:14 prefetch.2.10.7: 'SRR11978531' is valid 2020-07-14T01:27:14 prefetch.2.10.7: 1) 'SRR11978531' was downloaded successfully 2020-07-14T01:27:14 prefetch.2.10.7: 'SRR11978531' has 0 unresolved dependencies Read 9631154 spots for SRR11978531/SRR11978531.sra Written 9631154 spots for SRR11978531/SRR11978531.sra 2020-07-14T01:28:01 prefetch.2.10.7: 1) Downloading 'SRR11978532'... 2020-07-14T01:28:01 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:29:29 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:29:30 prefetch.2.10.7: 'SRR11978532' is valid 2020-07-14T01:29:30 prefetch.2.10.7: 1) 'SRR11978532' was downloaded successfully 2020-07-14T01:29:30 prefetch.2.10.7: 'SRR11978532' has 0 unresolved dependencies Read 9910989 spots for SRR11978532/SRR11978532.sra Written 9910989 spots for SRR11978532/SRR11978532.sra 2020-07-14T01:30:17 prefetch.2.10.7: 1) Downloading 'SRR11978533'... 2020-07-14T01:30:17 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:31:29 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:31:30 prefetch.2.10.7: 'SRR11978533' is valid 2020-07-14T01:31:30 prefetch.2.10.7: 1) 'SRR11978533' was downloaded successfully 2020-07-14T01:31:30 prefetch.2.10.7: 'SRR11978533' has 0 unresolved dependencies Read 9725571 spots for SRR11978533/SRR11978533.sra Written 9725571 spots for SRR11978533/SRR11978533.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627420 ("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: 00:06:48 39014224 reads; of these: 39014224 (100.00%) were unpaired; of these: 32228253 (82.61%) aligned 0 times 4949026 (12.69%) aligned exactly 1 time 1836945 (4.71%) aligned >1 times 17.39% overall alignment rate Time searching: 00:06:48 Overall time: 00:06:48 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] 1172892 / 6785971 = 0.1728 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 10:41:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.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 10:41:25: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:41:25: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:41:32: 1000000 INFO @ Tue, 14 Jul 2020 10:41:38: 2000000 INFO @ Tue, 14 Jul 2020 10:41:45: 3000000 INFO @ Tue, 14 Jul 2020 10:41:51: 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 10:41:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.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 10:41:55: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:41:55: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:41:58: 5000000 INFO @ Tue, 14 Jul 2020 10:42:02: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 10:42:02: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 10:42:02: #1 total tags in treatment: 5613079 INFO @ Tue, 14 Jul 2020 10:42:02: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:42:02: #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 10:42:02: 1000000 INFO @ Tue, 14 Jul 2020 10:42:02: #1 tags after filtering in treatment: 5613079 INFO @ Tue, 14 Jul 2020 10:42:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:42:02: #1 finished! INFO @ Tue, 14 Jul 2020 10:42:02: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:42:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:42:02: #2 number of paired peaks: 349 WARNING @ Tue, 14 Jul 2020 10:42:02: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Tue, 14 Jul 2020 10:42:02: start model_add_line... INFO @ Tue, 14 Jul 2020 10:42:02: start X-correlation... INFO @ Tue, 14 Jul 2020 10:42:02: end of X-cor INFO @ Tue, 14 Jul 2020 10:42:02: #2 finished! INFO @ Tue, 14 Jul 2020 10:42:02: #2 predicted fragment length is 62 bps INFO @ Tue, 14 Jul 2020 10:42:02: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 14 Jul 2020 10:42:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.05_model.r WARNING @ Tue, 14 Jul 2020 10:42:02: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:42:02: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 14 Jul 2020 10:42:02: #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 10:42:02: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:42:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:42:07: 2000000 INFO @ Tue, 14 Jul 2020 10:42:13: 3000000 INFO @ Tue, 14 Jul 2020 10:42:14: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:42:19: 4000000 INFO @ Tue, 14 Jul 2020 10:42:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:42:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:42:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.05_summits.bed INFO @ Tue, 14 Jul 2020 10:42:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1770 records, 4 fields): 4 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 10:42:25: 5000000 INFO @ Tue, 14 Jul 2020 10:42:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.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 10:42:25: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:42:25: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:42:28: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 10:42:28: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 10:42:28: #1 total tags in treatment: 5613079 INFO @ Tue, 14 Jul 2020 10:42:28: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:42:28: #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 10:42:28: #1 tags after filtering in treatment: 5613079 INFO @ Tue, 14 Jul 2020 10:42:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:42:28: #1 finished! INFO @ Tue, 14 Jul 2020 10:42:28: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:42:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:42:29: #2 number of paired peaks: 349 WARNING @ Tue, 14 Jul 2020 10:42:29: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Tue, 14 Jul 2020 10:42:29: start model_add_line... INFO @ Tue, 14 Jul 2020 10:42:29: start X-correlation... INFO @ Tue, 14 Jul 2020 10:42:29: end of X-cor INFO @ Tue, 14 Jul 2020 10:42:29: #2 finished! INFO @ Tue, 14 Jul 2020 10:42:29: #2 predicted fragment length is 62 bps INFO @ Tue, 14 Jul 2020 10:42:29: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 14 Jul 2020 10:42:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.10_model.r WARNING @ Tue, 14 Jul 2020 10:42:29: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:42:29: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 14 Jul 2020 10:42:29: #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 10:42:29: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:42:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:42:32: 1000000 INFO @ Tue, 14 Jul 2020 10:42:38: 2000000 INFO @ Tue, 14 Jul 2020 10:42:41: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:42:45: 3000000 INFO @ Tue, 14 Jul 2020 10:42:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:42:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:42:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.10_summits.bed INFO @ Tue, 14 Jul 2020 10:42:47: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (645 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:42:51: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:42:57: 5000000 INFO @ Tue, 14 Jul 2020 10:43:01: #1 tag size is determined as 62 bps INFO @ Tue, 14 Jul 2020 10:43:01: #1 tag size = 62 INFO @ Tue, 14 Jul 2020 10:43:01: #1 total tags in treatment: 5613079 INFO @ Tue, 14 Jul 2020 10:43:01: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:43:01: #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 10:43:01: #1 tags after filtering in treatment: 5613079 INFO @ Tue, 14 Jul 2020 10:43:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:43:01: #1 finished! INFO @ Tue, 14 Jul 2020 10:43:01: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:43:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:43:02: #2 number of paired peaks: 349 WARNING @ Tue, 14 Jul 2020 10:43:02: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Tue, 14 Jul 2020 10:43:02: start model_add_line... INFO @ Tue, 14 Jul 2020 10:43:02: start X-correlation... INFO @ Tue, 14 Jul 2020 10:43:02: end of X-cor INFO @ Tue, 14 Jul 2020 10:43:02: #2 finished! INFO @ Tue, 14 Jul 2020 10:43:02: #2 predicted fragment length is 62 bps INFO @ Tue, 14 Jul 2020 10:43:02: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 14 Jul 2020 10:43:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.20_model.r WARNING @ Tue, 14 Jul 2020 10:43:02: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:43:02: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 14 Jul 2020 10:43:02: #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 10:43:02: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:43:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:43:14: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:43:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:43:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:43:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521302/SRX8521302.20_summits.bed INFO @ Tue, 14 Jul 2020 10:43:19: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (156 records, 4 fields): 1 millis CompletedMACS2peakCalling