[2023-03-19 01:50:01,866] [INFO] DFAST_QC pipeline started.
[2023-03-19 01:50:01,866] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 01:50:01,866] [INFO] DQC Reference Directory: /var/lib/cwl/stg4af92af9-47ca-4739-9444-f758dc25743e/dqc_reference
[2023-03-19 01:50:03,562] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 01:50:03,564] [INFO] Task started: Prodigal
[2023-03-19 01:50:03,564] [INFO] Running command: cat /var/lib/cwl/stg6fc063c4-58bd-4cf2-b82b-6ea96114c0ee/OceanDNA-b6673.fa | prodigal -d OceanDNA-b6673/cds.fna -a OceanDNA-b6673/protein.faa -g 11 -q > /dev/null
[2023-03-19 01:50:26,473] [INFO] Task succeeded: Prodigal
[2023-03-19 01:50:26,474] [INFO] Task started: HMMsearch
[2023-03-19 01:50:26,474] [INFO] Running command: hmmsearch --tblout OceanDNA-b6673/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4af92af9-47ca-4739-9444-f758dc25743e/dqc_reference/reference_markers.hmm OceanDNA-b6673/protein.faa > /dev/null
[2023-03-19 01:50:26,669] [INFO] Task succeeded: HMMsearch
[2023-03-19 01:50:26,670] [INFO] Found 6/6 markers.
[2023-03-19 01:50:26,691] [INFO] Query marker FASTA was written to OceanDNA-b6673/markers.fasta
[2023-03-19 01:50:26,692] [INFO] Task started: Blastn
[2023-03-19 01:50:26,692] [INFO] Running command: blastn -query OceanDNA-b6673/markers.fasta -db /var/lib/cwl/stg4af92af9-47ca-4739-9444-f758dc25743e/dqc_reference/reference_markers.fasta -out OceanDNA-b6673/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:50:27,264] [INFO] Task succeeded: Blastn
[2023-03-19 01:50:27,265] [INFO] Selected 18 target genomes.
[2023-03-19 01:50:27,266] [INFO] Target genome list was writen to OceanDNA-b6673/target_genomes.txt
[2023-03-19 01:50:27,280] [INFO] Task started: fastANI
[2023-03-19 01:50:27,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fc063c4-58bd-4cf2-b82b-6ea96114c0ee/OceanDNA-b6673.fa --refList OceanDNA-b6673/target_genomes.txt --output OceanDNA-b6673/fastani_result.tsv --threads 1
[2023-03-19 01:50:39,875] [INFO] Task succeeded: fastANI
[2023-03-19 01:50:39,875] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4af92af9-47ca-4739-9444-f758dc25743e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 01:50:39,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4af92af9-47ca-4739-9444-f758dc25743e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 01:50:39,886] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 01:50:39,886] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 01:50:39,886] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Cellulophaga tyrosinoxydans	strain=DSM 21164	GCA_900176415.1	504486	504486	type	True	78.3008	391	1177	95	below_threshold
Cellulophaga algicola	strain=DSM 14237	GCA_000186265.1	59600	59600	type	True	78.0252	373	1177	95	below_threshold
Cellulophaga baltica	strain=DSM 24729	GCA_900102165.1	76594	76594	type	True	78.0178	371	1177	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	76.7999	209	1177	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	76.7712	180	1177	95	below_threshold
Maribacter vaceletii	strain=DSM 25230	GCA_003634105.1	1206816	1206816	type	True	76.6882	201	1177	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	76.6394	162	1177	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	76.627	190	1177	95	below_threshold
Arenibacter algicola	strain=TG409	GCA_000733925.1	616991	616991	type	True	76.6267	127	1177	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	76.5904	178	1177	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	76.5776	195	1177	95	below_threshold
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	76.4613	94	1177	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.3908	110	1177	95	below_threshold
Kordia algicida	strain=OT-1	GCA_000154725.1	221066	221066	type	True	76.1575	71	1177	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	76.1134	109	1177	95	below_threshold
Haloflavibacter putidus	strain=PLHSN227	GCA_006546625.1	2576776	2576776	type	True	76.0664	62	1177	95	below_threshold
Aestuariivivens sediminis	strain=S-DT1-15	GCA_022662105.1	2913557	2913557	type	True	76.0504	53	1177	95	below_threshold
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	75.9018	105	1177	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 01:50:39,887] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6673/tc_result.tsv
[2023-03-19 01:50:39,887] [INFO] ===== Taxonomy check completed =====
[2023-03-19 01:50:39,887] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 01:50:39,887] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4af92af9-47ca-4739-9444-f758dc25743e/dqc_reference/checkm_data
[2023-03-19 01:50:39,888] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 01:50:39,949] [INFO] Task started: CheckM
[2023-03-19 01:50:39,949] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6673/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6673/checkm_input OceanDNA-b6673/checkm_result
[2023-03-19 01:51:36,806] [INFO] Task succeeded: CheckM
[2023-03-19 01:51:36,806] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 01:51:36,820] [INFO] ===== Completeness check finished =====
[2023-03-19 01:51:36,820] [INFO] ===== Start GTDB Search =====
[2023-03-19 01:51:36,820] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6673/markers.fasta)
[2023-03-19 01:51:36,821] [INFO] Task started: Blastn
[2023-03-19 01:51:36,821] [INFO] Running command: blastn -query OceanDNA-b6673/markers.fasta -db /var/lib/cwl/stg4af92af9-47ca-4739-9444-f758dc25743e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6673/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 01:51:37,637] [INFO] Task succeeded: Blastn
[2023-03-19 01:51:37,638] [INFO] Selected 14 target genomes.
[2023-03-19 01:51:37,638] [INFO] Target genome list was writen to OceanDNA-b6673/target_genomes_gtdb.txt
[2023-03-19 01:51:37,646] [INFO] Task started: fastANI
[2023-03-19 01:51:37,646] [INFO] Running command: fastANI --query /var/lib/cwl/stg6fc063c4-58bd-4cf2-b82b-6ea96114c0ee/OceanDNA-b6673.fa --refList OceanDNA-b6673/target_genomes_gtdb.txt --output OceanDNA-b6673/fastani_result_gtdb.tsv --threads 1
[2023-03-19 01:51:47,584] [INFO] Task succeeded: fastANI
[2023-03-19 01:51:47,592] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 01:51:47,592] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_000799565.1	s__Cellulophaga sp000799565	90.523	1012	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019021925.1	s__Cellulophaga sp019021925	78.3668	356	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176415.1	s__Cellulophaga tyrosinoxydans	78.3106	390	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009797025.1	s__Cellulophaga sp009797025	78.1313	360	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186265.1	s__Cellulophaga algicola	78.0252	373	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	98.35	98.34	0.88	0.87	3	-
GCF_900102165.1	s__Cellulophaga baltica	78.01	372	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	97.62	97.40	0.90	0.89	7	-
GCF_018861125.1	s__Cellulophaga baltica_A	77.8679	337	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000190595.1	s__Cellulophaga lytica	76.9335	201	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	99.01	98.71	0.94	0.93	6	-
GCF_900119145.1	s__Cellulophaga fucicola	76.8533	194	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634105.1	s__Maribacter_B vaceletii	76.6882	201	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142175.1	s__Maribacter aquivivus	76.6015	177	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001913155.1	s__Maribacter hydrothermalis	76.587	194	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900141885.1	s__Mesonia phycicola	75.9018	105	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050085.1	s__Pricia antarctica_A	75.7699	73	1177	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pricia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 01:51:47,594] [INFO] GTDB search result was written to OceanDNA-b6673/result_gtdb.tsv
[2023-03-19 01:51:47,597] [INFO] ===== GTDB Search completed =====
[2023-03-19 01:51:47,599] [INFO] DFAST_QC result json was written to OceanDNA-b6673/dqc_result.json
[2023-03-19 01:51:47,599] [INFO] DFAST_QC completed!
[2023-03-19 01:51:47,599] [INFO] Total running time: 0h1m46s