Job ID = 6627306 SRX = SRX8521364 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:56:26 prefetch.2.10.7: 1) Downloading 'SRR11978122'... 2020-07-14T01:56:26 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:58:59 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:59:00 prefetch.2.10.7: 'SRR11978122' is valid 2020-07-14T01:59:00 prefetch.2.10.7: 1) 'SRR11978122' was downloaded successfully 2020-07-14T01:59:00 prefetch.2.10.7: 'SRR11978122' has 0 unresolved dependencies Read 11237630 spots for SRR11978122/SRR11978122.sra Written 11237630 spots for SRR11978122/SRR11978122.sra 2020-07-14T01:59:51 prefetch.2.10.7: 1) Downloading 'SRR11978123'... 2020-07-14T01:59:51 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:01:12 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:01:12 prefetch.2.10.7: 'SRR11978123' is valid 2020-07-14T02:01:12 prefetch.2.10.7: 1) 'SRR11978123' was downloaded successfully 2020-07-14T02:01:12 prefetch.2.10.7: 'SRR11978123' has 0 unresolved dependencies Read 11074219 spots for SRR11978123/SRR11978123.sra Written 11074219 spots for SRR11978123/SRR11978123.sra 2020-07-14T02:02:04 prefetch.2.10.7: 1) Downloading 'SRR11978124'... 2020-07-14T02:02:04 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:06:10 prefetch.2.10.7: HTTPS download failed 2020-07-14T02:06:10 prefetch.2.10.7: 1) failed to download SRR11978124 2020-07-14T02:06:24 prefetch.2.10.7: 1) Downloading 'SRR11978124'... 2020-07-14T02:06:24 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:06:24 prefetch.2.10.7: Continue download of 'SRR11978124' from 307018768 2020-07-14T02:06:33 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:06:34 prefetch.2.10.7: 'SRR11978124' is valid 2020-07-14T02:06:34 prefetch.2.10.7: 1) 'SRR11978124' was downloaded successfully 2020-07-14T02:06:34 prefetch.2.10.7: 'SRR11978124' has 0 unresolved dependencies Read 11334937 spots for SRR11978124/SRR11978124.sra Written 11334937 spots for SRR11978124/SRR11978124.sra 2020-07-14T02:07:31 prefetch.2.10.7: 1) Downloading 'SRR11978125'... 2020-07-14T02:07:31 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:08:47 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:08:48 prefetch.2.10.7: 'SRR11978125' is valid 2020-07-14T02:08:48 prefetch.2.10.7: 1) 'SRR11978125' was downloaded successfully 2020-07-14T02:08:48 prefetch.2.10.7: 'SRR11978125' has 0 unresolved dependencies Read 11126116 spots for SRR11978125/SRR11978125.sra Written 11126116 spots for SRR11978125/SRR11978125.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627554 ("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: 00:08:23 44772902 reads; of these: 44772902 (100.00%) were unpaired; of these: 36094501 (80.62%) aligned 0 times 6366481 (14.22%) aligned exactly 1 time 2311920 (5.16%) aligned >1 times 19.38% overall alignment rate Time searching: 00:08:23 Overall time: 00:08:23 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] 1594519 / 8678401 = 0.1837 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 11:21:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.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 11:21:13: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:21:13: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:21:20: 1000000 INFO @ Tue, 14 Jul 2020 11:21:26: 2000000 INFO @ Tue, 14 Jul 2020 11:21:32: 3000000 INFO @ Tue, 14 Jul 2020 11:21:38: 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 11:21:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.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 11:21:43: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:21:43: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:21:44: 5000000 INFO @ Tue, 14 Jul 2020 11:21:51: 6000000 INFO @ Tue, 14 Jul 2020 11:21:51: 1000000 INFO @ Tue, 14 Jul 2020 11:21:57: 7000000 INFO @ Tue, 14 Jul 2020 11:21:58: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 11:21:58: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 11:21:58: #1 total tags in treatment: 7083882 INFO @ Tue, 14 Jul 2020 11:21:58: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:21:58: #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 11:21:58: #1 tags after filtering in treatment: 7083882 INFO @ Tue, 14 Jul 2020 11:21:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:21:58: #1 finished! INFO @ Tue, 14 Jul 2020 11:21:58: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:21:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:21:59: #2 number of paired peaks: 266 WARNING @ Tue, 14 Jul 2020 11:21:59: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Tue, 14 Jul 2020 11:21:59: start model_add_line... INFO @ Tue, 14 Jul 2020 11:21:59: start X-correlation... INFO @ Tue, 14 Jul 2020 11:21:59: end of X-cor INFO @ Tue, 14 Jul 2020 11:21:59: #2 finished! INFO @ Tue, 14 Jul 2020 11:21:59: #2 predicted fragment length is 54 bps INFO @ Tue, 14 Jul 2020 11:21:59: #2 alternative fragment length(s) may be 54,537 bps INFO @ Tue, 14 Jul 2020 11:21:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.05_model.r WARNING @ Tue, 14 Jul 2020 11:21:59: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:21:59: #2 You may need to consider one of the other alternative d(s): 54,537 WARNING @ Tue, 14 Jul 2020 11:21:59: #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 11:21:59: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:21:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:21:59: 2000000 INFO @ Tue, 14 Jul 2020 11:22:06: 3000000 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 11:22:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.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 11:22:13: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:22:13: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:22:14: 4000000 INFO @ Tue, 14 Jul 2020 11:22:14: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:22:21: 1000000 INFO @ Tue, 14 Jul 2020 11:22:22: 5000000 INFO @ Tue, 14 Jul 2020 11:22:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:22:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:22:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.05_summits.bed INFO @ Tue, 14 Jul 2020 11:22:23: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1996 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:22:30: 6000000 INFO @ Tue, 14 Jul 2020 11:22:30: 2000000 INFO @ Tue, 14 Jul 2020 11:22:37: 3000000 INFO @ Tue, 14 Jul 2020 11:22:37: 7000000 INFO @ Tue, 14 Jul 2020 11:22:38: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 11:22:38: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 11:22:38: #1 total tags in treatment: 7083882 INFO @ Tue, 14 Jul 2020 11:22:38: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:22:38: #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 11:22:38: #1 tags after filtering in treatment: 7083882 INFO @ Tue, 14 Jul 2020 11:22:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:22:38: #1 finished! INFO @ Tue, 14 Jul 2020 11:22:38: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:22:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:22:38: #2 number of paired peaks: 266 WARNING @ Tue, 14 Jul 2020 11:22:38: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Tue, 14 Jul 2020 11:22:38: start model_add_line... INFO @ Tue, 14 Jul 2020 11:22:39: start X-correlation... INFO @ Tue, 14 Jul 2020 11:22:39: end of X-cor INFO @ Tue, 14 Jul 2020 11:22:39: #2 finished! INFO @ Tue, 14 Jul 2020 11:22:39: #2 predicted fragment length is 54 bps INFO @ Tue, 14 Jul 2020 11:22:39: #2 alternative fragment length(s) may be 54,537 bps INFO @ Tue, 14 Jul 2020 11:22:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.10_model.r WARNING @ Tue, 14 Jul 2020 11:22:39: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:22:39: #2 You may need to consider one of the other alternative d(s): 54,537 WARNING @ Tue, 14 Jul 2020 11:22:39: #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 11:22:39: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:22:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:22:44: 4000000 INFO @ Tue, 14 Jul 2020 11:22:50: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:22:54: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:22:57: 6000000 INFO @ Tue, 14 Jul 2020 11:23:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:23:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:23:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.10_summits.bed INFO @ Tue, 14 Jul 2020 11:23:02: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (720 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:23:03: 7000000 INFO @ Tue, 14 Jul 2020 11:23:04: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 11:23:04: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 11:23:04: #1 total tags in treatment: 7083882 INFO @ Tue, 14 Jul 2020 11:23:04: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:23:04: #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 11:23:04: #1 tags after filtering in treatment: 7083882 INFO @ Tue, 14 Jul 2020 11:23:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:23:04: #1 finished! INFO @ Tue, 14 Jul 2020 11:23:04: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:23:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:23:04: #2 number of paired peaks: 266 WARNING @ Tue, 14 Jul 2020 11:23:04: Fewer paired peaks (266) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 266 pairs to build model! INFO @ Tue, 14 Jul 2020 11:23:04: start model_add_line... INFO @ Tue, 14 Jul 2020 11:23:05: start X-correlation... INFO @ Tue, 14 Jul 2020 11:23:05: end of X-cor INFO @ Tue, 14 Jul 2020 11:23:05: #2 finished! INFO @ Tue, 14 Jul 2020 11:23:05: #2 predicted fragment length is 54 bps INFO @ Tue, 14 Jul 2020 11:23:05: #2 alternative fragment length(s) may be 54,537 bps INFO @ Tue, 14 Jul 2020 11:23:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.20_model.r WARNING @ Tue, 14 Jul 2020 11:23:05: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:23:05: #2 You may need to consider one of the other alternative d(s): 54,537 WARNING @ Tue, 14 Jul 2020 11:23:05: #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 11:23:05: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:23:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:23:20: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:23:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:23:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:23:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521364/SRX8521364.20_summits.bed INFO @ Tue, 14 Jul 2020 11:23:28: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (152 records, 4 fields): 2 millis CompletedMACS2peakCalling