Job ID = 6365943 SRX = SRX043875 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:32:51 prefetch.2.10.7: 1) Downloading 'SRR107345'... 2020-06-15T22:32:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:33:29 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:33:29 prefetch.2.10.7: 'SRR107345' is valid 2020-06-15T22:33:29 prefetch.2.10.7: 1) 'SRR107345' was downloaded successfully Read 2864459 spots for SRR107345/SRR107345.sra Written 2864459 spots for SRR107345/SRR107345.sra 2020-06-15T22:33:48 prefetch.2.10.7: 1) Downloading 'SRR107346'... 2020-06-15T22:33:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:34:15 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:34:15 prefetch.2.10.7: 'SRR107346' is valid 2020-06-15T22:34:15 prefetch.2.10.7: 1) 'SRR107346' was downloaded successfully Read 3379553 spots for SRR107346/SRR107346.sra Written 3379553 spots for SRR107346/SRR107346.sra 2020-06-15T22:34:36 prefetch.2.10.7: 1) Downloading 'SRR107347'... 2020-06-15T22:34:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:34:52 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:34:53 prefetch.2.10.7: 'SRR107347' is valid 2020-06-15T22:34:53 prefetch.2.10.7: 1) 'SRR107347' was downloaded successfully Read 1231928 spots for SRR107347/SRR107347.sra Written 1231928 spots for SRR107347/SRR107347.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: 00:00:36 7475940 reads; of these: 7475940 (100.00%) were unpaired; of these: 6665085 (89.15%) aligned 0 times 709579 (9.49%) aligned exactly 1 time 101276 (1.35%) aligned >1 times 10.85% overall alignment rate Time searching: 00:00:36 Overall time: 00:00:36 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 21178 / 810855 = 0.0261 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, 16 Jun 2020 07:36:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 16 Jun 2020 07:36:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:36:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:36:26: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:36:26: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:36:26: #1 total tags in treatment: 789677 INFO @ Tue, 16 Jun 2020 07:36:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:36:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:36:26: #1 tags after filtering in treatment: 789677 INFO @ Tue, 16 Jun 2020 07:36:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:36:26: #1 finished! INFO @ Tue, 16 Jun 2020 07:36:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:36:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:36:26: #2 number of paired peaks: 276 WARNING @ Tue, 16 Jun 2020 07:36:26: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Tue, 16 Jun 2020 07:36:26: start model_add_line... INFO @ Tue, 16 Jun 2020 07:36:26: start X-correlation... INFO @ Tue, 16 Jun 2020 07:36:26: end of X-cor INFO @ Tue, 16 Jun 2020 07:36:26: #2 finished! INFO @ Tue, 16 Jun 2020 07:36:26: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 07:36:26: #2 alternative fragment length(s) may be 39,87,105,117,419,459,491,516,565 bps INFO @ Tue, 16 Jun 2020 07:36:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.05_model.r WARNING @ Tue, 16 Jun 2020 07:36:26: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:36:26: #2 You may need to consider one of the other alternative d(s): 39,87,105,117,419,459,491,516,565 WARNING @ Tue, 16 Jun 2020 07:36:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:36:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:36:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:36:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:36:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:36:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:36:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.05_summits.bed INFO @ Tue, 16 Jun 2020 07:36:29: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (49 records, 4 fields): 1 millis CompletedMACS2peakCalling 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, 16 Jun 2020 07:36:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 16 Jun 2020 07:36:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:36:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:36:56: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:36:56: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:36:56: #1 total tags in treatment: 789677 INFO @ Tue, 16 Jun 2020 07:36:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:36:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:36:56: #1 tags after filtering in treatment: 789677 INFO @ Tue, 16 Jun 2020 07:36:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:36:56: #1 finished! INFO @ Tue, 16 Jun 2020 07:36:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:36:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:36:56: #2 number of paired peaks: 276 WARNING @ Tue, 16 Jun 2020 07:36:56: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Tue, 16 Jun 2020 07:36:56: start model_add_line... INFO @ Tue, 16 Jun 2020 07:36:56: start X-correlation... INFO @ Tue, 16 Jun 2020 07:36:56: end of X-cor INFO @ Tue, 16 Jun 2020 07:36:56: #2 finished! INFO @ Tue, 16 Jun 2020 07:36:56: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 07:36:56: #2 alternative fragment length(s) may be 39,87,105,117,419,459,491,516,565 bps INFO @ Tue, 16 Jun 2020 07:36:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.10_model.r WARNING @ Tue, 16 Jun 2020 07:36:56: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:36:56: #2 You may need to consider one of the other alternative d(s): 39,87,105,117,419,459,491,516,565 WARNING @ Tue, 16 Jun 2020 07:36:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:36:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:36:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:36:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:36:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:36:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:36:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.10_summits.bed INFO @ Tue, 16 Jun 2020 07:36:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (17 records, 4 fields): 13 millis CompletedMACS2peakCalling 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, 16 Jun 2020 07:37:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.bam'] # control file = None # effective genome size = 9.00e+07 # 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, 16 Jun 2020 07:37:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:37:21: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:37:26: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:37:26: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:37:26: #1 total tags in treatment: 789677 INFO @ Tue, 16 Jun 2020 07:37:26: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:37:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 07:37:26: #1 tags after filtering in treatment: 789677 INFO @ Tue, 16 Jun 2020 07:37:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:37:26: #1 finished! INFO @ Tue, 16 Jun 2020 07:37:26: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:37:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:37:26: #2 number of paired peaks: 276 WARNING @ Tue, 16 Jun 2020 07:37:26: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Tue, 16 Jun 2020 07:37:26: start model_add_line... INFO @ Tue, 16 Jun 2020 07:37:26: start X-correlation... INFO @ Tue, 16 Jun 2020 07:37:26: end of X-cor INFO @ Tue, 16 Jun 2020 07:37:26: #2 finished! INFO @ Tue, 16 Jun 2020 07:37:26: #2 predicted fragment length is 39 bps INFO @ Tue, 16 Jun 2020 07:37:26: #2 alternative fragment length(s) may be 39,87,105,117,419,459,491,516,565 bps INFO @ Tue, 16 Jun 2020 07:37:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.20_model.r WARNING @ Tue, 16 Jun 2020 07:37:26: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:37:26: #2 You may need to consider one of the other alternative d(s): 39,87,105,117,419,459,491,516,565 WARNING @ Tue, 16 Jun 2020 07:37:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 07:37:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:37:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:37:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:37:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:37:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:37:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043875/SRX043875.20_summits.bed INFO @ Tue, 16 Jun 2020 07:37:29: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (5 records, 4 fields): 1 millis CompletedMACS2peakCalling