Job ID = 6627576 SRX = SRX8521410 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T03:03:33 prefetch.2.10.7: 1) Downloading 'SRR11978382'... 2020-07-14T03:03:33 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:19:33 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:19:34 prefetch.2.10.7: 'SRR11978382' is valid 2020-07-14T03:19:34 prefetch.2.10.7: 1) 'SRR11978382' was downloaded successfully 2020-07-14T03:19:34 prefetch.2.10.7: 'SRR11978382' has 0 unresolved dependencies Read 11773188 spots for SRR11978382/SRR11978382.sra Written 11773188 spots for SRR11978382/SRR11978382.sra 2020-07-14T03:20:28 prefetch.2.10.7: 1) Downloading 'SRR11978383'... 2020-07-14T03:20:28 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:25:31 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:25:32 prefetch.2.10.7: 'SRR11978383' is valid 2020-07-14T03:25:32 prefetch.2.10.7: 1) 'SRR11978383' was downloaded successfully 2020-07-14T03:25:32 prefetch.2.10.7: 'SRR11978383' has 0 unresolved dependencies Read 11450179 spots for SRR11978383/SRR11978383.sra Written 11450179 spots for SRR11978383/SRR11978383.sra 2020-07-14T03:26:24 prefetch.2.10.7: 1) Downloading 'SRR11978384'... 2020-07-14T03:26:24 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:27:45 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:27:46 prefetch.2.10.7: 'SRR11978384' is valid 2020-07-14T03:27:46 prefetch.2.10.7: 1) 'SRR11978384' was downloaded successfully 2020-07-14T03:27:46 prefetch.2.10.7: 'SRR11978384' has 0 unresolved dependencies Read 11567272 spots for SRR11978384/SRR11978384.sra Written 11567272 spots for SRR11978384/SRR11978384.sra 2020-07-14T03:28:38 prefetch.2.10.7: 1) Downloading 'SRR11978385'... 2020-07-14T03:28:38 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:29:49 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:29:50 prefetch.2.10.7: 'SRR11978385' is valid 2020-07-14T03:29:50 prefetch.2.10.7: 1) 'SRR11978385' was downloaded successfully 2020-07-14T03:29:50 prefetch.2.10.7: 'SRR11978385' has 0 unresolved dependencies Read 11640199 spots for SRR11978385/SRR11978385.sra Written 11640199 spots for SRR11978385/SRR11978385.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627828 ("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: 00:06:38 46430838 reads; of these: 46430838 (100.00%) were unpaired; of these: 41028473 (88.36%) aligned 0 times 4139178 (8.91%) aligned exactly 1 time 1263187 (2.72%) aligned >1 times 11.64% overall alignment rate Time searching: 00:06:38 Overall time: 00:06:38 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] 831064 / 5402365 = 0.1538 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 12:39:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.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 12:39:27: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:39:27: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:39:32: 1000000 INFO @ Tue, 14 Jul 2020 12:39:37: 2000000 INFO @ Tue, 14 Jul 2020 12:39:42: 3000000 INFO @ Tue, 14 Jul 2020 12:39:47: 4000000 INFO @ Tue, 14 Jul 2020 12:39:50: #1 tag size is determined as 56 bps INFO @ Tue, 14 Jul 2020 12:39:50: #1 tag size = 56 INFO @ Tue, 14 Jul 2020 12:39:50: #1 total tags in treatment: 4571301 INFO @ Tue, 14 Jul 2020 12:39:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:39:50: #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 12:39:50: #1 tags after filtering in treatment: 4571301 INFO @ Tue, 14 Jul 2020 12:39:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:39:50: #1 finished! INFO @ Tue, 14 Jul 2020 12:39:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:39:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:39:50: #2 number of paired peaks: 396 WARNING @ Tue, 14 Jul 2020 12:39:50: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Tue, 14 Jul 2020 12:39:50: start model_add_line... INFO @ Tue, 14 Jul 2020 12:39:50: start X-correlation... INFO @ Tue, 14 Jul 2020 12:39:50: end of X-cor INFO @ Tue, 14 Jul 2020 12:39:50: #2 finished! INFO @ Tue, 14 Jul 2020 12:39:50: #2 predicted fragment length is 53 bps INFO @ Tue, 14 Jul 2020 12:39:50: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 14 Jul 2020 12:39:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.05_model.r WARNING @ Tue, 14 Jul 2020 12:39:50: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:39:50: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 14 Jul 2020 12:39:50: #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 12:39:50: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:39:50: #3 Pre-compute pvalue-qvalue table... 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 12:39:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.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 12:39:57: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:39:57: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:40:00: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:40:04: 1000000 INFO @ Tue, 14 Jul 2020 12:40:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:40:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:40:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.05_summits.bed INFO @ Tue, 14 Jul 2020 12:40:05: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1261 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:40:09: 2000000 INFO @ Tue, 14 Jul 2020 12:40:14: 3000000 INFO @ Tue, 14 Jul 2020 12:40:19: 4000000 INFO @ Tue, 14 Jul 2020 12:40:22: #1 tag size is determined as 56 bps INFO @ Tue, 14 Jul 2020 12:40:22: #1 tag size = 56 INFO @ Tue, 14 Jul 2020 12:40:22: #1 total tags in treatment: 4571301 INFO @ Tue, 14 Jul 2020 12:40:22: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:40:22: #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 12:40:22: #1 tags after filtering in treatment: 4571301 INFO @ Tue, 14 Jul 2020 12:40:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:40:22: #1 finished! INFO @ Tue, 14 Jul 2020 12:40:22: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:40:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:40:23: #2 number of paired peaks: 396 WARNING @ Tue, 14 Jul 2020 12:40:23: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Tue, 14 Jul 2020 12:40:23: start model_add_line... INFO @ Tue, 14 Jul 2020 12:40:23: start X-correlation... INFO @ Tue, 14 Jul 2020 12:40:23: end of X-cor INFO @ Tue, 14 Jul 2020 12:40:23: #2 finished! INFO @ Tue, 14 Jul 2020 12:40:23: #2 predicted fragment length is 53 bps INFO @ Tue, 14 Jul 2020 12:40:23: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 14 Jul 2020 12:40:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.10_model.r WARNING @ Tue, 14 Jul 2020 12:40:23: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:40:23: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 14 Jul 2020 12:40:23: #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 12:40:23: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:40:23: #3 Pre-compute pvalue-qvalue table... 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 12:40:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.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 12:40:27: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:40:27: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:40:32: 1000000 INFO @ Tue, 14 Jul 2020 12:40:33: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:40:37: 2000000 INFO @ Tue, 14 Jul 2020 12:40:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:40:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:40:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.10_summits.bed INFO @ Tue, 14 Jul 2020 12:40:38: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (425 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:40:42: 3000000 INFO @ Tue, 14 Jul 2020 12:40:47: 4000000 INFO @ Tue, 14 Jul 2020 12:40:50: #1 tag size is determined as 56 bps INFO @ Tue, 14 Jul 2020 12:40:50: #1 tag size = 56 INFO @ Tue, 14 Jul 2020 12:40:50: #1 total tags in treatment: 4571301 INFO @ Tue, 14 Jul 2020 12:40:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:40:50: #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 12:40:50: #1 tags after filtering in treatment: 4571301 INFO @ Tue, 14 Jul 2020 12:40:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:40:50: #1 finished! INFO @ Tue, 14 Jul 2020 12:40:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:40:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:40:51: #2 number of paired peaks: 396 WARNING @ Tue, 14 Jul 2020 12:40:51: Fewer paired peaks (396) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 396 pairs to build model! INFO @ Tue, 14 Jul 2020 12:40:51: start model_add_line... INFO @ Tue, 14 Jul 2020 12:40:51: start X-correlation... INFO @ Tue, 14 Jul 2020 12:40:51: end of X-cor INFO @ Tue, 14 Jul 2020 12:40:51: #2 finished! INFO @ Tue, 14 Jul 2020 12:40:51: #2 predicted fragment length is 53 bps INFO @ Tue, 14 Jul 2020 12:40:51: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 14 Jul 2020 12:40:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.20_model.r WARNING @ Tue, 14 Jul 2020 12:40:51: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:40:51: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 14 Jul 2020 12:40:51: #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 12:40:51: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:40:51: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:41:01: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:41:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:41:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:41:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521410/SRX8521410.20_summits.bed INFO @ Tue, 14 Jul 2020 12:41:05: Done! pass1 - making usageList (5 chroms): 0 millis pass2 - checking and writing primary data (81 records, 4 fields): 2 millis CompletedMACS2peakCalling