Job ID = 6627114 SRX = SRX8521291 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T00:57:32 prefetch.2.10.7: 1) Downloading 'SRR11978458'... 2020-07-14T00:57:32 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:00:08 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:00:09 prefetch.2.10.7: 'SRR11978458' is valid 2020-07-14T01:00:09 prefetch.2.10.7: 1) 'SRR11978458' was downloaded successfully 2020-07-14T01:00:09 prefetch.2.10.7: 'SRR11978458' has 0 unresolved dependencies Read 16833035 spots for SRR11978458/SRR11978458.sra Written 16833035 spots for SRR11978458/SRR11978458.sra 2020-07-14T01:01:14 prefetch.2.10.7: 1) Downloading 'SRR11978459'... 2020-07-14T01:01:14 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:03:24 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:03:24 prefetch.2.10.7: 'SRR11978459' is valid 2020-07-14T01:03:24 prefetch.2.10.7: 1) 'SRR11978459' was downloaded successfully 2020-07-14T01:03:24 prefetch.2.10.7: 'SRR11978459' has 0 unresolved dependencies Read 16633363 spots for SRR11978459/SRR11978459.sra Written 16633363 spots for SRR11978459/SRR11978459.sra 2020-07-14T01:04:32 prefetch.2.10.7: 1) Downloading 'SRR11978460'... 2020-07-14T01:04:32 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:06:10 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:06:11 prefetch.2.10.7: 'SRR11978460' is valid 2020-07-14T01:06:11 prefetch.2.10.7: 1) 'SRR11978460' was downloaded successfully 2020-07-14T01:06:11 prefetch.2.10.7: 'SRR11978460' has 0 unresolved dependencies Read 17160732 spots for SRR11978460/SRR11978460.sra Written 17160732 spots for SRR11978460/SRR11978460.sra 2020-07-14T01:07:23 prefetch.2.10.7: 1) Downloading 'SRR11978461'... 2020-07-14T01:07:23 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:08:51 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:08:52 prefetch.2.10.7: 'SRR11978461' is valid 2020-07-14T01:08:52 prefetch.2.10.7: 1) 'SRR11978461' was downloaded successfully 2020-07-14T01:08:52 prefetch.2.10.7: 'SRR11978461' has 0 unresolved dependencies Read 17005969 spots for SRR11978461/SRR11978461.sra Written 17005969 spots for SRR11978461/SRR11978461.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627362 ("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: 00:10:09 67633099 reads; of these: 67633099 (100.00%) were unpaired; of these: 56905491 (84.14%) aligned 0 times 8328726 (12.31%) aligned exactly 1 time 2398882 (3.55%) aligned >1 times 15.86% overall alignment rate Time searching: 00:10:09 Overall time: 00:10:09 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] 3113733 / 10727608 = 0.2903 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 10:23:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.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 10:23:35: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:23:35: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:23:41: 1000000 INFO @ Tue, 14 Jul 2020 10:23:47: 2000000 INFO @ Tue, 14 Jul 2020 10:23:53: 3000000 INFO @ Tue, 14 Jul 2020 10:23:58: 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 10:24:04: 5000000 INFO @ Tue, 14 Jul 2020 10:24:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.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 10:24:06: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:24:06: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:24:11: 6000000 INFO @ Tue, 14 Jul 2020 10:24:12: 1000000 INFO @ Tue, 14 Jul 2020 10:24:17: 7000000 INFO @ Tue, 14 Jul 2020 10:24:19: 2000000 INFO @ Tue, 14 Jul 2020 10:24:22: #1 tag size is determined as 64 bps INFO @ Tue, 14 Jul 2020 10:24:22: #1 tag size = 64 INFO @ Tue, 14 Jul 2020 10:24:22: #1 total tags in treatment: 7613875 INFO @ Tue, 14 Jul 2020 10:24:22: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:24:22: #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 10:24:22: #1 tags after filtering in treatment: 7613875 INFO @ Tue, 14 Jul 2020 10:24:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:24:22: #1 finished! INFO @ Tue, 14 Jul 2020 10:24:22: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:24:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:24:22: #2 number of paired peaks: 435 WARNING @ Tue, 14 Jul 2020 10:24:22: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Tue, 14 Jul 2020 10:24:22: start model_add_line... INFO @ Tue, 14 Jul 2020 10:24:22: start X-correlation... INFO @ Tue, 14 Jul 2020 10:24:22: end of X-cor INFO @ Tue, 14 Jul 2020 10:24:22: #2 finished! INFO @ Tue, 14 Jul 2020 10:24:22: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 10:24:22: #2 alternative fragment length(s) may be 60 bps INFO @ Tue, 14 Jul 2020 10:24:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.05_model.r WARNING @ Tue, 14 Jul 2020 10:24:22: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:24:22: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Tue, 14 Jul 2020 10:24:22: #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 10:24:22: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:24:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:24:26: 3000000 INFO @ Tue, 14 Jul 2020 10:24:32: 4000000 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 10:24:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.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 10:24:35: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:24:35: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:24:38: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:24:38: 5000000 INFO @ Tue, 14 Jul 2020 10:24:42: 1000000 INFO @ Tue, 14 Jul 2020 10:24:45: 6000000 INFO @ Tue, 14 Jul 2020 10:24:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:24:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:24:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.05_summits.bed INFO @ Tue, 14 Jul 2020 10:24:46: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3507 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:24:49: 2000000 INFO @ Tue, 14 Jul 2020 10:24:52: 7000000 INFO @ Tue, 14 Jul 2020 10:24:56: 3000000 INFO @ Tue, 14 Jul 2020 10:24:56: #1 tag size is determined as 64 bps INFO @ Tue, 14 Jul 2020 10:24:56: #1 tag size = 64 INFO @ Tue, 14 Jul 2020 10:24:56: #1 total tags in treatment: 7613875 INFO @ Tue, 14 Jul 2020 10:24:56: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:24:56: #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 10:24:56: #1 tags after filtering in treatment: 7613875 INFO @ Tue, 14 Jul 2020 10:24:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:24:56: #1 finished! INFO @ Tue, 14 Jul 2020 10:24:56: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:24:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:24:57: #2 number of paired peaks: 435 WARNING @ Tue, 14 Jul 2020 10:24:57: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Tue, 14 Jul 2020 10:24:57: start model_add_line... INFO @ Tue, 14 Jul 2020 10:24:57: start X-correlation... INFO @ Tue, 14 Jul 2020 10:24:57: end of X-cor INFO @ Tue, 14 Jul 2020 10:24:57: #2 finished! INFO @ Tue, 14 Jul 2020 10:24:57: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 10:24:57: #2 alternative fragment length(s) may be 60 bps INFO @ Tue, 14 Jul 2020 10:24:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.10_model.r WARNING @ Tue, 14 Jul 2020 10:24:57: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:24:57: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Tue, 14 Jul 2020 10:24:57: #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 10:24:57: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:24:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:25:02: 4000000 INFO @ Tue, 14 Jul 2020 10:25:08: 5000000 INFO @ Tue, 14 Jul 2020 10:25:12: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:25:14: 6000000 INFO @ Tue, 14 Jul 2020 10:25:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:25:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:25:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.10_summits.bed INFO @ Tue, 14 Jul 2020 10:25:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1344 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:25:21: 7000000 INFO @ Tue, 14 Jul 2020 10:25:25: #1 tag size is determined as 64 bps INFO @ Tue, 14 Jul 2020 10:25:25: #1 tag size = 64 INFO @ Tue, 14 Jul 2020 10:25:25: #1 total tags in treatment: 7613875 INFO @ Tue, 14 Jul 2020 10:25:25: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:25:25: #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 10:25:25: #1 tags after filtering in treatment: 7613875 INFO @ Tue, 14 Jul 2020 10:25:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:25:25: #1 finished! INFO @ Tue, 14 Jul 2020 10:25:25: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:25:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:25:25: #2 number of paired peaks: 435 WARNING @ Tue, 14 Jul 2020 10:25:25: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Tue, 14 Jul 2020 10:25:25: start model_add_line... INFO @ Tue, 14 Jul 2020 10:25:25: start X-correlation... INFO @ Tue, 14 Jul 2020 10:25:25: end of X-cor INFO @ Tue, 14 Jul 2020 10:25:25: #2 finished! INFO @ Tue, 14 Jul 2020 10:25:25: #2 predicted fragment length is 60 bps INFO @ Tue, 14 Jul 2020 10:25:25: #2 alternative fragment length(s) may be 60 bps INFO @ Tue, 14 Jul 2020 10:25:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.20_model.r WARNING @ Tue, 14 Jul 2020 10:25:25: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:25:25: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Tue, 14 Jul 2020 10:25:25: #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 10:25:25: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:25:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:25:41: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:25:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:25:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:25:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521291/SRX8521291.20_summits.bed INFO @ Tue, 14 Jul 2020 10:25:49: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (266 records, 4 fields): 1 millis CompletedMACS2peakCalling