Job ID = 6627283 SRX = SRX8521347 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:49:59 prefetch.2.10.7: 1) Downloading 'SRR11978632'... 2020-07-14T01:49:59 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:52:04 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:52:05 prefetch.2.10.7: 'SRR11978632' is valid 2020-07-14T01:52:05 prefetch.2.10.7: 1) 'SRR11978632' was downloaded successfully 2020-07-14T01:52:05 prefetch.2.10.7: 'SRR11978632' has 0 unresolved dependencies Read 17232672 spots for SRR11978632/SRR11978632.sra Written 17232672 spots for SRR11978632/SRR11978632.sra 2020-07-14T01:53:15 prefetch.2.10.7: 1) Downloading 'SRR11978633'... 2020-07-14T01:53:15 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:55:34 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:55:35 prefetch.2.10.7: 'SRR11978633' is valid 2020-07-14T01:55:35 prefetch.2.10.7: 1) 'SRR11978633' was downloaded successfully 2020-07-14T01:55:35 prefetch.2.10.7: 'SRR11978633' has 0 unresolved dependencies Read 16854348 spots for SRR11978633/SRR11978633.sra Written 16854348 spots for SRR11978633/SRR11978633.sra 2020-07-14T01:56:44 prefetch.2.10.7: 1) Downloading 'SRR11978634'... 2020-07-14T01:56:44 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:59:26 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:59:27 prefetch.2.10.7: 'SRR11978634' is valid 2020-07-14T01:59:27 prefetch.2.10.7: 1) 'SRR11978634' was downloaded successfully 2020-07-14T01:59:27 prefetch.2.10.7: 'SRR11978634' has 0 unresolved dependencies Read 17452727 spots for SRR11978634/SRR11978634.sra Written 17452727 spots for SRR11978634/SRR11978634.sra 2020-07-14T02:00:43 prefetch.2.10.7: 1) Downloading 'SRR11978635'... 2020-07-14T02:00:43 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:02:45 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:02:46 prefetch.2.10.7: 'SRR11978635' is valid 2020-07-14T02:02:46 prefetch.2.10.7: 1) 'SRR11978635' was downloaded successfully 2020-07-14T02:02:46 prefetch.2.10.7: 'SRR11978635' has 0 unresolved dependencies Read 17487488 spots for SRR11978635/SRR11978635.sra Written 17487488 spots for SRR11978635/SRR11978635.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627557 ("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: 00:14:57 69027235 reads; of these: 69027235 (100.00%) were unpaired; of these: 56051694 (81.20%) aligned 0 times 8330202 (12.07%) aligned exactly 1 time 4645339 (6.73%) aligned >1 times 18.80% overall alignment rate Time searching: 00:14:57 Overall time: 00:14:57 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] 3512281 / 12975541 = 0.2707 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 11:22:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.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 11:22:59: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:22:59: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:23:06: 1000000 INFO @ Tue, 14 Jul 2020 11:23:13: 2000000 INFO @ Tue, 14 Jul 2020 11:23:19: 3000000 INFO @ Tue, 14 Jul 2020 11:23:26: 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 11:23:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.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 11:23:29: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:23:29: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:23:32: 5000000 INFO @ Tue, 14 Jul 2020 11:23:36: 1000000 INFO @ Tue, 14 Jul 2020 11:23:39: 6000000 INFO @ Tue, 14 Jul 2020 11:23:43: 2000000 INFO @ Tue, 14 Jul 2020 11:23:46: 7000000 INFO @ Tue, 14 Jul 2020 11:23:50: 3000000 INFO @ Tue, 14 Jul 2020 11:23:53: 8000000 INFO @ Tue, 14 Jul 2020 11:23:57: 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 11:23:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.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 11:23:59: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:23:59: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:24:00: 9000000 INFO @ Tue, 14 Jul 2020 11:24:03: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 11:24:03: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 11:24:03: #1 total tags in treatment: 9463260 INFO @ Tue, 14 Jul 2020 11:24:03: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:24:03: #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 11:24:03: #1 tags after filtering in treatment: 9463260 INFO @ Tue, 14 Jul 2020 11:24:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:24:03: #1 finished! INFO @ Tue, 14 Jul 2020 11:24:03: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:24:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:24:04: #2 number of paired peaks: 161 WARNING @ Tue, 14 Jul 2020 11:24:04: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Tue, 14 Jul 2020 11:24:04: start model_add_line... INFO @ Tue, 14 Jul 2020 11:24:04: 5000000 INFO @ Tue, 14 Jul 2020 11:24:04: start X-correlation... INFO @ Tue, 14 Jul 2020 11:24:04: end of X-cor INFO @ Tue, 14 Jul 2020 11:24:04: #2 finished! INFO @ Tue, 14 Jul 2020 11:24:04: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 11:24:04: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 11:24:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.05_model.r WARNING @ Tue, 14 Jul 2020 11:24:04: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:24:04: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 11:24:04: #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 11:24:04: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:24:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:24:06: 1000000 INFO @ Tue, 14 Jul 2020 11:24:11: 6000000 INFO @ Tue, 14 Jul 2020 11:24:12: 2000000 INFO @ Tue, 14 Jul 2020 11:24:18: 7000000 INFO @ Tue, 14 Jul 2020 11:24:18: 3000000 INFO @ Tue, 14 Jul 2020 11:24:22: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:24:24: 4000000 INFO @ Tue, 14 Jul 2020 11:24:24: 8000000 INFO @ Tue, 14 Jul 2020 11:24:31: 5000000 INFO @ Tue, 14 Jul 2020 11:24:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:24:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:24:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.05_summits.bed INFO @ Tue, 14 Jul 2020 11:24:31: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2030 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:24:31: 9000000 INFO @ Tue, 14 Jul 2020 11:24:34: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 11:24:34: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 11:24:34: #1 total tags in treatment: 9463260 INFO @ Tue, 14 Jul 2020 11:24:34: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:24:34: #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 11:24:35: #1 tags after filtering in treatment: 9463260 INFO @ Tue, 14 Jul 2020 11:24:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:24:35: #1 finished! INFO @ Tue, 14 Jul 2020 11:24:35: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:24:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:24:35: #2 number of paired peaks: 161 WARNING @ Tue, 14 Jul 2020 11:24:35: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Tue, 14 Jul 2020 11:24:35: start model_add_line... INFO @ Tue, 14 Jul 2020 11:24:35: start X-correlation... INFO @ Tue, 14 Jul 2020 11:24:35: end of X-cor INFO @ Tue, 14 Jul 2020 11:24:35: #2 finished! INFO @ Tue, 14 Jul 2020 11:24:35: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 11:24:35: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 11:24:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.10_model.r WARNING @ Tue, 14 Jul 2020 11:24:35: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:24:35: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 11:24:35: #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 11:24:35: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:24:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:24:37: 6000000 INFO @ Tue, 14 Jul 2020 11:24:43: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:24:49: 8000000 INFO @ Tue, 14 Jul 2020 11:24:53: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:24:54: 9000000 INFO @ Tue, 14 Jul 2020 11:24:57: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 11:24:57: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 11:24:57: #1 total tags in treatment: 9463260 INFO @ Tue, 14 Jul 2020 11:24:57: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:24:57: #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 11:24:57: #1 tags after filtering in treatment: 9463260 INFO @ Tue, 14 Jul 2020 11:24:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:24:57: #1 finished! INFO @ Tue, 14 Jul 2020 11:24:57: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:24:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:24:58: #2 number of paired peaks: 161 WARNING @ Tue, 14 Jul 2020 11:24:58: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Tue, 14 Jul 2020 11:24:58: start model_add_line... INFO @ Tue, 14 Jul 2020 11:24:58: start X-correlation... INFO @ Tue, 14 Jul 2020 11:24:58: end of X-cor INFO @ Tue, 14 Jul 2020 11:24:58: #2 finished! INFO @ Tue, 14 Jul 2020 11:24:58: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 11:24:58: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 11:24:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.20_model.r WARNING @ Tue, 14 Jul 2020 11:24:58: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:24:58: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 11:24:58: #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 11:24:58: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:24:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:25:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:25:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:25:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.10_summits.bed INFO @ Tue, 14 Jul 2020 11:25:03: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1114 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:25:16: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:25:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:25:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:25:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521347/SRX8521347.20_summits.bed INFO @ Tue, 14 Jul 2020 11:25:25: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (514 records, 4 fields): 1 millis CompletedMACS2peakCalling