Job ID = 6454409 SRX = SRX2035281 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:16:54 prefetch.2.10.7: 1) Downloading 'SRR4044405'... 2020-06-21T09:16:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:21:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:21:36 prefetch.2.10.7: 1) 'SRR4044405' was downloaded successfully 2020-06-21T09:21:36 prefetch.2.10.7: 'SRR4044405' has 0 unresolved dependencies Read 21933505 spots for SRR4044405/SRR4044405.sra Written 21933505 spots for SRR4044405/SRR4044405.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:02 21933505 reads; of these: 21933505 (100.00%) were unpaired; of these: 907776 (4.14%) aligned 0 times 17209055 (78.46%) aligned exactly 1 time 3816674 (17.40%) aligned >1 times 95.86% overall alignment rate Time searching: 00:08:02 Overall time: 00:08:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 5294824 / 21025729 = 0.2518 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 @ Sun, 21 Jun 2020 18:37:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.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 @ Sun, 21 Jun 2020 18:37:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:37:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:37:25: 1000000 INFO @ Sun, 21 Jun 2020 18:37:31: 2000000 INFO @ Sun, 21 Jun 2020 18:37:37: 3000000 INFO @ Sun, 21 Jun 2020 18:37:43: 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 @ Sun, 21 Jun 2020 18:37:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.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 @ Sun, 21 Jun 2020 18:37:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:37:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:37:49: 5000000 INFO @ Sun, 21 Jun 2020 18:37:56: 1000000 INFO @ Sun, 21 Jun 2020 18:37:56: 6000000 INFO @ Sun, 21 Jun 2020 18:38:02: 2000000 INFO @ Sun, 21 Jun 2020 18:38:03: 7000000 INFO @ Sun, 21 Jun 2020 18:38:09: 3000000 INFO @ Sun, 21 Jun 2020 18:38:09: 8000000 INFO @ Sun, 21 Jun 2020 18:38:16: 4000000 INFO @ Sun, 21 Jun 2020 18:38:16: 9000000 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 @ Sun, 21 Jun 2020 18:38:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.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 @ Sun, 21 Jun 2020 18:38:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:38:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:38:23: 10000000 INFO @ Sun, 21 Jun 2020 18:38:23: 5000000 INFO @ Sun, 21 Jun 2020 18:38:26: 1000000 INFO @ Sun, 21 Jun 2020 18:38:29: 11000000 INFO @ Sun, 21 Jun 2020 18:38:29: 6000000 INFO @ Sun, 21 Jun 2020 18:38:33: 2000000 INFO @ Sun, 21 Jun 2020 18:38:36: 12000000 INFO @ Sun, 21 Jun 2020 18:38:36: 7000000 INFO @ Sun, 21 Jun 2020 18:38:40: 3000000 INFO @ Sun, 21 Jun 2020 18:38:43: 8000000 INFO @ Sun, 21 Jun 2020 18:38:43: 13000000 INFO @ Sun, 21 Jun 2020 18:38:46: 4000000 INFO @ Sun, 21 Jun 2020 18:38:49: 9000000 INFO @ Sun, 21 Jun 2020 18:38:50: 14000000 INFO @ Sun, 21 Jun 2020 18:38:53: 5000000 INFO @ Sun, 21 Jun 2020 18:38:56: 10000000 INFO @ Sun, 21 Jun 2020 18:38:56: 15000000 INFO @ Sun, 21 Jun 2020 18:39:00: 6000000 INFO @ Sun, 21 Jun 2020 18:39:01: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 18:39:01: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 18:39:01: #1 total tags in treatment: 15730905 INFO @ Sun, 21 Jun 2020 18:39:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:39:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:39:02: #1 tags after filtering in treatment: 15730897 INFO @ Sun, 21 Jun 2020 18:39:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:39:02: #1 finished! INFO @ Sun, 21 Jun 2020 18:39:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:39:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:39:03: 11000000 INFO @ Sun, 21 Jun 2020 18:39:03: #2 number of paired peaks: 3262 INFO @ Sun, 21 Jun 2020 18:39:03: start model_add_line... INFO @ Sun, 21 Jun 2020 18:39:04: start X-correlation... INFO @ Sun, 21 Jun 2020 18:39:04: end of X-cor INFO @ Sun, 21 Jun 2020 18:39:04: #2 finished! INFO @ Sun, 21 Jun 2020 18:39:04: #2 predicted fragment length is 141 bps INFO @ Sun, 21 Jun 2020 18:39:04: #2 alternative fragment length(s) may be 141 bps INFO @ Sun, 21 Jun 2020 18:39:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.05_model.r WARNING @ Sun, 21 Jun 2020 18:39:04: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:39:04: #2 You may need to consider one of the other alternative d(s): 141 WARNING @ Sun, 21 Jun 2020 18:39:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:39:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:39:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:39:07: 7000000 INFO @ Sun, 21 Jun 2020 18:39:10: 12000000 INFO @ Sun, 21 Jun 2020 18:39:14: 8000000 INFO @ Sun, 21 Jun 2020 18:39:17: 13000000 INFO @ Sun, 21 Jun 2020 18:39:20: 9000000 INFO @ Sun, 21 Jun 2020 18:39:23: 14000000 INFO @ Sun, 21 Jun 2020 18:39:27: 10000000 INFO @ Sun, 21 Jun 2020 18:39:30: 15000000 INFO @ Sun, 21 Jun 2020 18:39:34: 11000000 INFO @ Sun, 21 Jun 2020 18:39:35: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 18:39:35: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 18:39:35: #1 total tags in treatment: 15730905 INFO @ Sun, 21 Jun 2020 18:39:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:39:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:39:36: #1 tags after filtering in treatment: 15730897 INFO @ Sun, 21 Jun 2020 18:39:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:39:36: #1 finished! INFO @ Sun, 21 Jun 2020 18:39:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:39:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:39:37: #2 number of paired peaks: 3262 INFO @ Sun, 21 Jun 2020 18:39:37: start model_add_line... INFO @ Sun, 21 Jun 2020 18:39:37: start X-correlation... INFO @ Sun, 21 Jun 2020 18:39:37: end of X-cor INFO @ Sun, 21 Jun 2020 18:39:37: #2 finished! INFO @ Sun, 21 Jun 2020 18:39:37: #2 predicted fragment length is 141 bps INFO @ Sun, 21 Jun 2020 18:39:37: #2 alternative fragment length(s) may be 141 bps INFO @ Sun, 21 Jun 2020 18:39:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.10_model.r WARNING @ Sun, 21 Jun 2020 18:39:37: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:39:37: #2 You may need to consider one of the other alternative d(s): 141 WARNING @ Sun, 21 Jun 2020 18:39:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:39:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:39:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:39:40: 12000000 INFO @ Sun, 21 Jun 2020 18:39:44: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:39:47: 13000000 INFO @ Sun, 21 Jun 2020 18:39:53: 14000000 INFO @ Sun, 21 Jun 2020 18:39:59: 15000000 INFO @ Sun, 21 Jun 2020 18:40:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:40:04: #1 tag size is determined as 76 bps INFO @ Sun, 21 Jun 2020 18:40:04: #1 tag size = 76 INFO @ Sun, 21 Jun 2020 18:40:04: #1 total tags in treatment: 15730905 INFO @ Sun, 21 Jun 2020 18:40:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:40:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 18:40:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:40:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.05_summits.bed INFO @ Sun, 21 Jun 2020 18:40:04: Done! INFO @ Sun, 21 Jun 2020 18:40:05: #1 tags after filtering in treatment: 15730897 INFO @ Sun, 21 Jun 2020 18:40:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:40:05: #1 finished! INFO @ Sun, 21 Jun 2020 18:40:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:40:05: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (550 chroms): 3 millis pass2 - checking and writing primary data (15353 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:40:06: #2 number of paired peaks: 3262 INFO @ Sun, 21 Jun 2020 18:40:06: start model_add_line... INFO @ Sun, 21 Jun 2020 18:40:06: start X-correlation... INFO @ Sun, 21 Jun 2020 18:40:06: end of X-cor INFO @ Sun, 21 Jun 2020 18:40:06: #2 finished! INFO @ Sun, 21 Jun 2020 18:40:06: #2 predicted fragment length is 141 bps INFO @ Sun, 21 Jun 2020 18:40:06: #2 alternative fragment length(s) may be 141 bps INFO @ Sun, 21 Jun 2020 18:40:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.20_model.r WARNING @ Sun, 21 Jun 2020 18:40:06: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:40:06: #2 You may need to consider one of the other alternative d(s): 141 WARNING @ Sun, 21 Jun 2020 18:40:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:40:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:40:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:40:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:40:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:40:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:40:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.10_summits.bed INFO @ Sun, 21 Jun 2020 18:40:39: Done! pass1 - making usageList (427 chroms): 2 millis pass2 - checking and writing primary data (11516 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:40:47: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:41:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:41:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:41:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2035281/SRX2035281.20_summits.bed INFO @ Sun, 21 Jun 2020 18:41:09: Done! pass1 - making usageList (261 chroms): 2 millis pass2 - checking and writing primary data (7685 records, 4 fields): 18 millis CompletedMACS2peakCalling