Job ID = 6627266 SRX = SRX8521335 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:43:35 prefetch.2.10.7: 1) Downloading 'SRR11978037'... 2020-07-14T01:43:35 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:44:25 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:44:25 prefetch.2.10.7: 'SRR11978037' is valid 2020-07-14T01:44:25 prefetch.2.10.7: 1) 'SRR11978037' was downloaded successfully 2020-07-14T01:44:25 prefetch.2.10.7: 'SRR11978037' has 0 unresolved dependencies Read 3202040 spots for SRR11978037/SRR11978037.sra Written 3202040 spots for SRR11978037/SRR11978037.sra 2020-07-14T01:44:50 prefetch.2.10.7: 1) Downloading 'SRR11978038'... 2020-07-14T01:44:50 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:45:20 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:45:21 prefetch.2.10.7: 'SRR11978038' is valid 2020-07-14T01:45:21 prefetch.2.10.7: 1) 'SRR11978038' was downloaded successfully 2020-07-14T01:45:21 prefetch.2.10.7: 'SRR11978038' has 0 unresolved dependencies Read 3072164 spots for SRR11978038/SRR11978038.sra Written 3072164 spots for SRR11978038/SRR11978038.sra 2020-07-14T01:45:51 prefetch.2.10.7: 1) Downloading 'SRR11978039'... 2020-07-14T01:45:51 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:55:42 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:55:42 prefetch.2.10.7: 'SRR11978039' is valid 2020-07-14T01:55:42 prefetch.2.10.7: 1) 'SRR11978039' was downloaded successfully 2020-07-14T01:55:42 prefetch.2.10.7: 'SRR11978039' has 0 unresolved dependencies Read 3381936 spots for SRR11978039/SRR11978039.sra Written 3381936 spots for SRR11978039/SRR11978039.sra 2020-07-14T01:56:04 prefetch.2.10.7: 1) Downloading 'SRR11978040'... 2020-07-14T01:56:04 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:56:59 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:57:00 prefetch.2.10.7: 'SRR11978040' is valid 2020-07-14T01:57:00 prefetch.2.10.7: 1) 'SRR11978040' was downloaded successfully 2020-07-14T01:57:00 prefetch.2.10.7: 'SRR11978040' has 0 unresolved dependencies Read 3382516 spots for SRR11978040/SRR11978040.sra Written 3382516 spots for SRR11978040/SRR11978040.sra 2020-07-14T01:57:26 prefetch.2.10.7: 1) Downloading 'SRR11978041'... 2020-07-14T01:57:26 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:58:46 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:58:46 prefetch.2.10.7: 'SRR11978041' is valid 2020-07-14T01:58:46 prefetch.2.10.7: 1) 'SRR11978041' was downloaded successfully 2020-07-14T01:58:46 prefetch.2.10.7: 'SRR11978041' has 0 unresolved dependencies Read 7481237 spots for SRR11978041/SRR11978041.sra Written 7481237 spots for SRR11978041/SRR11978041.sra 2020-07-14T01:59:25 prefetch.2.10.7: 1) Downloading 'SRR11978042'... 2020-07-14T01:59:25 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:03:03 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:03:04 prefetch.2.10.7: 'SRR11978042' is valid 2020-07-14T02:03:04 prefetch.2.10.7: 1) 'SRR11978042' was downloaded successfully 2020-07-14T02:03:04 prefetch.2.10.7: 'SRR11978042' has 0 unresolved dependencies Read 7277905 spots for SRR11978042/SRR11978042.sra Written 7277905 spots for SRR11978042/SRR11978042.sra 2020-07-14T02:03:51 prefetch.2.10.7: 1) Downloading 'SRR11978043'... 2020-07-14T02:03:51 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:04:54 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:04:55 prefetch.2.10.7: 'SRR11978043' is valid 2020-07-14T02:04:55 prefetch.2.10.7: 1) 'SRR11978043' was downloaded successfully 2020-07-14T02:04:55 prefetch.2.10.7: 'SRR11978043' has 0 unresolved dependencies Read 7754121 spots for SRR11978043/SRR11978043.sra Written 7754121 spots for SRR11978043/SRR11978043.sra 2020-07-14T02:05:31 prefetch.2.10.7: 1) Downloading 'SRR11978044'... 2020-07-14T02:05:31 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:06:32 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:06:33 prefetch.2.10.7: 'SRR11978044' is valid 2020-07-14T02:06:33 prefetch.2.10.7: 1) 'SRR11978044' was downloaded successfully 2020-07-14T02:06:33 prefetch.2.10.7: 'SRR11978044' has 0 unresolved dependencies Read 7628025 spots for SRR11978044/SRR11978044.sra Written 7628025 spots for SRR11978044/SRR11978044.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627541 ("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: 00:06:58 43179944 reads; of these: 43179944 (100.00%) were unpaired; of these: 37289760 (86.36%) aligned 0 times 4396038 (10.18%) aligned exactly 1 time 1494146 (3.46%) aligned >1 times 13.64% overall alignment rate Time searching: 00:06:58 Overall time: 00:06:58 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] 1012454 / 5890184 = 0.1719 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 11:16:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.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 11:16:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:16:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:16:46: 1000000 INFO @ Tue, 14 Jul 2020 11:16:54: 2000000 INFO @ Tue, 14 Jul 2020 11:17:02: 3000000 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 11:17:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.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 11:17:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:17:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:17:10: 4000000 INFO @ Tue, 14 Jul 2020 11:17:17: 1000000 INFO @ Tue, 14 Jul 2020 11:17:17: #1 tag size is determined as 65 bps INFO @ Tue, 14 Jul 2020 11:17:17: #1 tag size = 65 INFO @ Tue, 14 Jul 2020 11:17:17: #1 total tags in treatment: 4877730 INFO @ Tue, 14 Jul 2020 11:17:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:17:17: #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 11:17:17: #1 tags after filtering in treatment: 4877730 INFO @ Tue, 14 Jul 2020 11:17:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:17:17: #1 finished! INFO @ Tue, 14 Jul 2020 11:17:17: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:17:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:17:17: #2 number of paired peaks: 450 WARNING @ Tue, 14 Jul 2020 11:17:17: Fewer paired peaks (450) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 450 pairs to build model! INFO @ Tue, 14 Jul 2020 11:17:17: start model_add_line... INFO @ Tue, 14 Jul 2020 11:17:17: start X-correlation... INFO @ Tue, 14 Jul 2020 11:17:17: end of X-cor INFO @ Tue, 14 Jul 2020 11:17:17: #2 finished! INFO @ Tue, 14 Jul 2020 11:17:17: #2 predicted fragment length is 68 bps INFO @ Tue, 14 Jul 2020 11:17:17: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 14 Jul 2020 11:17:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.05_model.r WARNING @ Tue, 14 Jul 2020 11:17:17: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:17:17: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 14 Jul 2020 11:17:17: #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 11:17:17: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:17:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:17:25: 2000000 INFO @ Tue, 14 Jul 2020 11:17:28: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:17:33: 3000000 INFO @ Tue, 14 Jul 2020 11:17:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:17:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:17:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.05_summits.bed INFO @ Tue, 14 Jul 2020 11:17:34: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1616 records, 4 fields): 3 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 11:17:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.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 11:17:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:17:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:17:41: 4000000 INFO @ Tue, 14 Jul 2020 11:17:47: 1000000 INFO @ Tue, 14 Jul 2020 11:17:48: #1 tag size is determined as 65 bps INFO @ Tue, 14 Jul 2020 11:17:48: #1 tag size = 65 INFO @ Tue, 14 Jul 2020 11:17:48: #1 total tags in treatment: 4877730 INFO @ Tue, 14 Jul 2020 11:17:48: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:17:48: #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 11:17:48: #1 tags after filtering in treatment: 4877730 INFO @ Tue, 14 Jul 2020 11:17:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:17:48: #1 finished! INFO @ Tue, 14 Jul 2020 11:17:48: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:17:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:17:48: #2 number of paired peaks: 450 WARNING @ Tue, 14 Jul 2020 11:17:48: Fewer paired peaks (450) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 450 pairs to build model! INFO @ Tue, 14 Jul 2020 11:17:48: start model_add_line... INFO @ Tue, 14 Jul 2020 11:17:48: start X-correlation... INFO @ Tue, 14 Jul 2020 11:17:48: end of X-cor INFO @ Tue, 14 Jul 2020 11:17:48: #2 finished! INFO @ Tue, 14 Jul 2020 11:17:48: #2 predicted fragment length is 68 bps INFO @ Tue, 14 Jul 2020 11:17:48: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 14 Jul 2020 11:17:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.10_model.r WARNING @ Tue, 14 Jul 2020 11:17:48: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:17:48: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 14 Jul 2020 11:17:48: #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 11:17:48: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:17:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:17:55: 2000000 INFO @ Tue, 14 Jul 2020 11:17:59: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:18:03: 3000000 INFO @ Tue, 14 Jul 2020 11:18:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:18:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:18:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.10_summits.bed INFO @ Tue, 14 Jul 2020 11:18:04: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (661 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:18:11: 4000000 INFO @ Tue, 14 Jul 2020 11:18:17: #1 tag size is determined as 65 bps INFO @ Tue, 14 Jul 2020 11:18:17: #1 tag size = 65 INFO @ Tue, 14 Jul 2020 11:18:17: #1 total tags in treatment: 4877730 INFO @ Tue, 14 Jul 2020 11:18:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:18:17: #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 11:18:18: #1 tags after filtering in treatment: 4877730 INFO @ Tue, 14 Jul 2020 11:18:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:18:18: #1 finished! INFO @ Tue, 14 Jul 2020 11:18:18: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:18:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:18:18: #2 number of paired peaks: 450 WARNING @ Tue, 14 Jul 2020 11:18:18: Fewer paired peaks (450) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 450 pairs to build model! INFO @ Tue, 14 Jul 2020 11:18:18: start model_add_line... INFO @ Tue, 14 Jul 2020 11:18:18: start X-correlation... INFO @ Tue, 14 Jul 2020 11:18:18: end of X-cor INFO @ Tue, 14 Jul 2020 11:18:18: #2 finished! INFO @ Tue, 14 Jul 2020 11:18:18: #2 predicted fragment length is 68 bps INFO @ Tue, 14 Jul 2020 11:18:18: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 14 Jul 2020 11:18:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.20_model.r WARNING @ Tue, 14 Jul 2020 11:18:18: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:18:18: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 14 Jul 2020 11:18:18: #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 11:18:18: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:18:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:18:28: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:18:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:18:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:18:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521335/SRX8521335.20_summits.bed INFO @ Tue, 14 Jul 2020 11:18:34: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (172 records, 4 fields): 2 millis CompletedMACS2peakCalling