Job ID = 6627156 SRX = SRX8521299 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:22:05 prefetch.2.10.7: 1) Downloading 'SRR11978514'... 2020-07-14T01:22:05 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:22:43 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:22:43 prefetch.2.10.7: 'SRR11978514' is valid 2020-07-14T01:22:43 prefetch.2.10.7: 1) 'SRR11978514' was downloaded successfully 2020-07-14T01:22:43 prefetch.2.10.7: 'SRR11978514' has 0 unresolved dependencies Read 2928227 spots for SRR11978514/SRR11978514.sra Written 2928227 spots for SRR11978514/SRR11978514.sra 2020-07-14T01:23:08 prefetch.2.10.7: 1) Downloading 'SRR11978515'... 2020-07-14T01:23:08 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:23:41 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:23:41 prefetch.2.10.7: 'SRR11978515' is valid 2020-07-14T01:23:41 prefetch.2.10.7: 1) 'SRR11978515' was downloaded successfully 2020-07-14T01:23:41 prefetch.2.10.7: 'SRR11978515' has 0 unresolved dependencies Read 2681055 spots for SRR11978515/SRR11978515.sra Written 2681055 spots for SRR11978515/SRR11978515.sra 2020-07-14T01:24:04 prefetch.2.10.7: 1) Downloading 'SRR11978516'... 2020-07-14T01:24:04 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:24:44 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:24:44 prefetch.2.10.7: 'SRR11978516' is valid 2020-07-14T01:24:44 prefetch.2.10.7: 1) 'SRR11978516' was downloaded successfully 2020-07-14T01:24:44 prefetch.2.10.7: 'SRR11978516' has 0 unresolved dependencies Read 2951718 spots for SRR11978516/SRR11978516.sra Written 2951718 spots for SRR11978516/SRR11978516.sra 2020-07-14T01:25:05 prefetch.2.10.7: 1) Downloading 'SRR11978517'... 2020-07-14T01:25:05 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:25:37 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:25:37 prefetch.2.10.7: 'SRR11978517' is valid 2020-07-14T01:25:37 prefetch.2.10.7: 1) 'SRR11978517' was downloaded successfully 2020-07-14T01:25:37 prefetch.2.10.7: 'SRR11978517' has 0 unresolved dependencies Read 3030054 spots for SRR11978517/SRR11978517.sra Written 3030054 spots for SRR11978517/SRR11978517.sra 2020-07-14T01:26:02 prefetch.2.10.7: 1) Downloading 'SRR11978518'... 2020-07-14T01:26:02 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:27:37 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:27:38 prefetch.2.10.7: 'SRR11978518' is valid 2020-07-14T01:27:38 prefetch.2.10.7: 1) 'SRR11978518' was downloaded successfully 2020-07-14T01:27:38 prefetch.2.10.7: 'SRR11978518' has 0 unresolved dependencies Read 10353485 spots for SRR11978518/SRR11978518.sra Written 10353485 spots for SRR11978518/SRR11978518.sra 2020-07-14T01:28:23 prefetch.2.10.7: 1) Downloading 'SRR11978519'... 2020-07-14T01:28:23 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:29:48 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:29:48 prefetch.2.10.7: 'SRR11978519' is valid 2020-07-14T01:29:48 prefetch.2.10.7: 1) 'SRR11978519' was downloaded successfully 2020-07-14T01:29:48 prefetch.2.10.7: 'SRR11978519' has 0 unresolved dependencies Read 9699889 spots for SRR11978519/SRR11978519.sra Written 9699889 spots for SRR11978519/SRR11978519.sra 2020-07-14T01:30:31 prefetch.2.10.7: 1) Downloading 'SRR11978520'... 2020-07-14T01:30:31 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:31:56 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:31:57 prefetch.2.10.7: 'SRR11978520' is valid 2020-07-14T01:31:57 prefetch.2.10.7: 1) 'SRR11978520' was downloaded successfully 2020-07-14T01:31:57 prefetch.2.10.7: 'SRR11978520' has 0 unresolved dependencies Read 10404212 spots for SRR11978520/SRR11978520.sra Written 10404212 spots for SRR11978520/SRR11978520.sra 2020-07-14T01:32:46 prefetch.2.10.7: 1) Downloading 'SRR11978521'... 2020-07-14T01:32:46 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:34:29 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:34:30 prefetch.2.10.7: 'SRR11978521' is valid 2020-07-14T01:34:30 prefetch.2.10.7: 1) 'SRR11978521' was downloaded successfully 2020-07-14T01:34:30 prefetch.2.10.7: 'SRR11978521' has 0 unresolved dependencies Read 10300706 spots for SRR11978521/SRR11978521.sra Written 10300706 spots for SRR11978521/SRR11978521.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627433 ("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: 00:09:11 52349346 reads; of these: 52349346 (100.00%) were unpaired; of these: 43235406 (82.59%) aligned 0 times 6593865 (12.60%) aligned exactly 1 time 2520075 (4.81%) aligned >1 times 17.41% overall alignment rate Time searching: 00:09:11 Overall time: 00:09:11 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] 1730735 / 9113940 = 0.1899 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 10:47:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.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 10:47:51: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:47:51: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:47:57: 1000000 INFO @ Tue, 14 Jul 2020 10:48:03: 2000000 INFO @ Tue, 14 Jul 2020 10:48:09: 3000000 INFO @ Tue, 14 Jul 2020 10:48:15: 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 10:48:21: 5000000 INFO @ Tue, 14 Jul 2020 10:48:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.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 10:48:21: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:48:21: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:48:27: 6000000 INFO @ Tue, 14 Jul 2020 10:48:28: 1000000 INFO @ Tue, 14 Jul 2020 10:48:33: 7000000 INFO @ Tue, 14 Jul 2020 10:48:35: 2000000 INFO @ Tue, 14 Jul 2020 10:48:36: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 10:48:36: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 10:48:36: #1 total tags in treatment: 7383205 INFO @ Tue, 14 Jul 2020 10:48:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:48:36: #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 10:48:36: #1 tags after filtering in treatment: 7383205 INFO @ Tue, 14 Jul 2020 10:48:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:48:36: #1 finished! INFO @ Tue, 14 Jul 2020 10:48:36: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:48:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:48:37: #2 number of paired peaks: 357 WARNING @ Tue, 14 Jul 2020 10:48:37: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Tue, 14 Jul 2020 10:48:37: start model_add_line... INFO @ Tue, 14 Jul 2020 10:48:37: start X-correlation... INFO @ Tue, 14 Jul 2020 10:48:37: end of X-cor INFO @ Tue, 14 Jul 2020 10:48:37: #2 finished! INFO @ Tue, 14 Jul 2020 10:48:37: #2 predicted fragment length is 64 bps INFO @ Tue, 14 Jul 2020 10:48:37: #2 alternative fragment length(s) may be 64 bps INFO @ Tue, 14 Jul 2020 10:48:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.05_model.r WARNING @ Tue, 14 Jul 2020 10:48:37: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:48:37: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Tue, 14 Jul 2020 10:48:37: #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 10:48:37: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:48:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:48:41: 3000000 INFO @ Tue, 14 Jul 2020 10:48:47: 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 10:48:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.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 10:48:51: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:48:51: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:48:52: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:48:53: 5000000 INFO @ Tue, 14 Jul 2020 10:48:58: 1000000 INFO @ Tue, 14 Jul 2020 10:48:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:48:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:48:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.05_summits.bed INFO @ Tue, 14 Jul 2020 10:48:59: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2590 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:49:00: 6000000 INFO @ Tue, 14 Jul 2020 10:49:04: 2000000 INFO @ Tue, 14 Jul 2020 10:49:06: 7000000 INFO @ Tue, 14 Jul 2020 10:49:09: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 10:49:09: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 10:49:09: #1 total tags in treatment: 7383205 INFO @ Tue, 14 Jul 2020 10:49:09: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:49:09: #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 10:49:09: #1 tags after filtering in treatment: 7383205 INFO @ Tue, 14 Jul 2020 10:49:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:49:09: #1 finished! INFO @ Tue, 14 Jul 2020 10:49:09: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:49:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:49:10: #2 number of paired peaks: 357 WARNING @ Tue, 14 Jul 2020 10:49:10: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Tue, 14 Jul 2020 10:49:10: start model_add_line... INFO @ Tue, 14 Jul 2020 10:49:10: start X-correlation... INFO @ Tue, 14 Jul 2020 10:49:10: end of X-cor INFO @ Tue, 14 Jul 2020 10:49:10: #2 finished! INFO @ Tue, 14 Jul 2020 10:49:10: #2 predicted fragment length is 64 bps INFO @ Tue, 14 Jul 2020 10:49:10: #2 alternative fragment length(s) may be 64 bps INFO @ Tue, 14 Jul 2020 10:49:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.10_model.r WARNING @ Tue, 14 Jul 2020 10:49:10: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:49:10: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Tue, 14 Jul 2020 10:49:10: #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 10:49:10: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:49:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:49:11: 3000000 INFO @ Tue, 14 Jul 2020 10:49:17: 4000000 INFO @ Tue, 14 Jul 2020 10:49:23: 5000000 INFO @ Tue, 14 Jul 2020 10:49:25: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:49:30: 6000000 INFO @ Tue, 14 Jul 2020 10:49:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:49:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:49:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.10_summits.bed INFO @ Tue, 14 Jul 2020 10:49:33: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1070 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:49:36: 7000000 INFO @ Tue, 14 Jul 2020 10:49:38: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 10:49:38: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 10:49:38: #1 total tags in treatment: 7383205 INFO @ Tue, 14 Jul 2020 10:49:38: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:49:38: #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 10:49:38: #1 tags after filtering in treatment: 7383205 INFO @ Tue, 14 Jul 2020 10:49:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:49:38: #1 finished! INFO @ Tue, 14 Jul 2020 10:49:38: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:49:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:49:39: #2 number of paired peaks: 357 WARNING @ Tue, 14 Jul 2020 10:49:39: Fewer paired peaks (357) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 357 pairs to build model! INFO @ Tue, 14 Jul 2020 10:49:39: start model_add_line... INFO @ Tue, 14 Jul 2020 10:49:39: start X-correlation... INFO @ Tue, 14 Jul 2020 10:49:39: end of X-cor INFO @ Tue, 14 Jul 2020 10:49:39: #2 finished! INFO @ Tue, 14 Jul 2020 10:49:39: #2 predicted fragment length is 64 bps INFO @ Tue, 14 Jul 2020 10:49:39: #2 alternative fragment length(s) may be 64 bps INFO @ Tue, 14 Jul 2020 10:49:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.20_model.r WARNING @ Tue, 14 Jul 2020 10:49:39: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:49:39: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Tue, 14 Jul 2020 10:49:39: #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 10:49:39: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:49:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:49:54: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:50:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:50:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:50:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521299/SRX8521299.20_summits.bed INFO @ Tue, 14 Jul 2020 10:50:02: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (312 records, 4 fields): 1 millis CompletedMACS2peakCalling