Job ID = 6627246 SRX = SRX8521322 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:35:57 prefetch.2.10.7: 1) Downloading 'SRR11977957'... 2020-07-14T01:35:57 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:37:03 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:37:03 prefetch.2.10.7: 'SRR11977957' is valid 2020-07-14T01:37:03 prefetch.2.10.7: 1) 'SRR11977957' was downloaded successfully 2020-07-14T01:37:03 prefetch.2.10.7: 'SRR11977957' has 0 unresolved dependencies Read 10195106 spots for SRR11977957/SRR11977957.sra Written 10195106 spots for SRR11977957/SRR11977957.sra 2020-07-14T01:37:54 prefetch.2.10.7: 1) Downloading 'SRR11977958'... 2020-07-14T01:37:54 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:38:57 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:38:57 prefetch.2.10.7: 'SRR11977958' is valid 2020-07-14T01:38:57 prefetch.2.10.7: 1) 'SRR11977958' was downloaded successfully 2020-07-14T01:38:57 prefetch.2.10.7: 'SRR11977958' has 0 unresolved dependencies Read 10097520 spots for SRR11977958/SRR11977958.sra Written 10097520 spots for SRR11977958/SRR11977958.sra 2020-07-14T01:39:42 prefetch.2.10.7: 1) Downloading 'SRR11977959'... 2020-07-14T01:39:42 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:40:39 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:40:40 prefetch.2.10.7: 'SRR11977959' is valid 2020-07-14T01:40:40 prefetch.2.10.7: 1) 'SRR11977959' was downloaded successfully 2020-07-14T01:40:40 prefetch.2.10.7: 'SRR11977959' has 0 unresolved dependencies Read 10228285 spots for SRR11977959/SRR11977959.sra Written 10228285 spots for SRR11977959/SRR11977959.sra 2020-07-14T01:41:30 prefetch.2.10.7: 1) Downloading 'SRR11977960'... 2020-07-14T01:41:30 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:43:20 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:43:21 prefetch.2.10.7: 'SRR11977960' is valid 2020-07-14T01:43:21 prefetch.2.10.7: 1) 'SRR11977960' was downloaded successfully 2020-07-14T01:43:21 prefetch.2.10.7: 'SRR11977960' has 0 unresolved dependencies Read 10417393 spots for SRR11977960/SRR11977960.sra Written 10417393 spots for SRR11977960/SRR11977960.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627448 ("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: 00:05:37 40938304 reads; of these: 40938304 (100.00%) were unpaired; of these: 36579378 (89.35%) aligned 0 times 3334285 (8.14%) aligned exactly 1 time 1024641 (2.50%) aligned >1 times 10.65% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:37 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] 719171 / 4358926 = 0.1650 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 10:51:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.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 10:51:28: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:51:28: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:51:35: 1000000 INFO @ Tue, 14 Jul 2020 10:51:42: 2000000 INFO @ Tue, 14 Jul 2020 10:51:51: 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 10:51:56: #1 tag size is determined as 59 bps INFO @ Tue, 14 Jul 2020 10:51:56: #1 tag size = 59 INFO @ Tue, 14 Jul 2020 10:51:56: #1 total tags in treatment: 3639755 INFO @ Tue, 14 Jul 2020 10:51:56: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:51:56: #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 10:51:56: #1 tags after filtering in treatment: 3639755 INFO @ Tue, 14 Jul 2020 10:51:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:51:56: #1 finished! INFO @ Tue, 14 Jul 2020 10:51:56: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:51:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:51:57: #2 number of paired peaks: 599 WARNING @ Tue, 14 Jul 2020 10:51:57: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Tue, 14 Jul 2020 10:51:57: start model_add_line... INFO @ Tue, 14 Jul 2020 10:51:57: start X-correlation... INFO @ Tue, 14 Jul 2020 10:51:57: end of X-cor INFO @ Tue, 14 Jul 2020 10:51:57: #2 finished! INFO @ Tue, 14 Jul 2020 10:51:57: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 10:51:57: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 14 Jul 2020 10:51:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.05_model.r WARNING @ Tue, 14 Jul 2020 10:51:57: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:51:57: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 14 Jul 2020 10:51:57: #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 10:51:57: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:51:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:51:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.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 10:51:58: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:51:58: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:52:04: 1000000 INFO @ Tue, 14 Jul 2020 10:52:05: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:52:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:52:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:52:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.05_summits.bed INFO @ Tue, 14 Jul 2020 10:52:10: Done! INFO @ Tue, 14 Jul 2020 10:52:10: 2000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1517 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:52:16: 3000000 INFO @ Tue, 14 Jul 2020 10:52:20: #1 tag size is determined as 59 bps INFO @ Tue, 14 Jul 2020 10:52:20: #1 tag size = 59 INFO @ Tue, 14 Jul 2020 10:52:20: #1 total tags in treatment: 3639755 INFO @ Tue, 14 Jul 2020 10:52:20: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:52:20: #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 10:52:20: #1 tags after filtering in treatment: 3639755 INFO @ Tue, 14 Jul 2020 10:52:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:52:20: #1 finished! INFO @ Tue, 14 Jul 2020 10:52:20: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:52:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:52:20: #2 number of paired peaks: 599 WARNING @ Tue, 14 Jul 2020 10:52:20: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Tue, 14 Jul 2020 10:52:20: start model_add_line... INFO @ Tue, 14 Jul 2020 10:52:20: start X-correlation... INFO @ Tue, 14 Jul 2020 10:52:20: end of X-cor INFO @ Tue, 14 Jul 2020 10:52:20: #2 finished! INFO @ Tue, 14 Jul 2020 10:52:20: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 10:52:20: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 14 Jul 2020 10:52:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.10_model.r WARNING @ Tue, 14 Jul 2020 10:52:20: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:52:20: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 14 Jul 2020 10:52:20: #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 10:52:20: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:52:20: #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 10:52:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.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 10:52:28: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:52:28: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:52:28: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:52:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:52:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:52:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.10_summits.bed INFO @ Tue, 14 Jul 2020 10:52:33: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (651 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:52:34: 1000000 INFO @ Tue, 14 Jul 2020 10:52:40: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:52:46: 3000000 INFO @ Tue, 14 Jul 2020 10:52:50: #1 tag size is determined as 59 bps INFO @ Tue, 14 Jul 2020 10:52:50: #1 tag size = 59 INFO @ Tue, 14 Jul 2020 10:52:50: #1 total tags in treatment: 3639755 INFO @ Tue, 14 Jul 2020 10:52:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:52:50: #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 10:52:50: #1 tags after filtering in treatment: 3639755 INFO @ Tue, 14 Jul 2020 10:52:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:52:50: #1 finished! INFO @ Tue, 14 Jul 2020 10:52:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:52:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:52:50: #2 number of paired peaks: 599 WARNING @ Tue, 14 Jul 2020 10:52:50: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Tue, 14 Jul 2020 10:52:50: start model_add_line... INFO @ Tue, 14 Jul 2020 10:52:50: start X-correlation... INFO @ Tue, 14 Jul 2020 10:52:50: end of X-cor INFO @ Tue, 14 Jul 2020 10:52:50: #2 finished! INFO @ Tue, 14 Jul 2020 10:52:50: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 10:52:50: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 14 Jul 2020 10:52:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.20_model.r WARNING @ Tue, 14 Jul 2020 10:52:51: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:52:51: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 14 Jul 2020 10:52:51: #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 10:52:51: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:52:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:52:59: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:53:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:53:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:53:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521322/SRX8521322.20_summits.bed INFO @ Tue, 14 Jul 2020 10:53:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (128 records, 4 fields): 1 millis CompletedMACS2peakCalling