[2024-01-24 13:55:58,156] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:58,158] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:58,158] [INFO] DQC Reference Directory: /var/lib/cwl/stgedfe2267-f076-4242-850d-9ca82a832e11/dqc_reference
[2024-01-24 13:55:59,401] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:59,401] [INFO] Task started: Prodigal
[2024-01-24 13:55:59,402] [INFO] Running command: gunzip -c /var/lib/cwl/stg97b55ea3-426f-4b23-84fa-09c65f34ccd5/GCF_013328345.1_ASM1332834v1_genomic.fna.gz | prodigal -d GCF_013328345.1_ASM1332834v1_genomic.fna/cds.fna -a GCF_013328345.1_ASM1332834v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:07,620] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:07,621] [INFO] Task started: HMMsearch
[2024-01-24 13:56:07,621] [INFO] Running command: hmmsearch --tblout GCF_013328345.1_ASM1332834v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgedfe2267-f076-4242-850d-9ca82a832e11/dqc_reference/reference_markers.hmm GCF_013328345.1_ASM1332834v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:07,875] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:07,877] [INFO] Found 6/6 markers.
[2024-01-24 13:56:07,917] [INFO] Query marker FASTA was written to GCF_013328345.1_ASM1332834v1_genomic.fna/markers.fasta
[2024-01-24 13:56:07,917] [INFO] Task started: Blastn
[2024-01-24 13:56:07,918] [INFO] Running command: blastn -query GCF_013328345.1_ASM1332834v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedfe2267-f076-4242-850d-9ca82a832e11/dqc_reference/reference_markers.fasta -out GCF_013328345.1_ASM1332834v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:08,669] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:08,681] [INFO] Selected 23 target genomes.
[2024-01-24 13:56:08,681] [INFO] Target genome list was writen to GCF_013328345.1_ASM1332834v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:08,733] [INFO] Task started: fastANI
[2024-01-24 13:56:08,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg97b55ea3-426f-4b23-84fa-09c65f34ccd5/GCF_013328345.1_ASM1332834v1_genomic.fna.gz --refList GCF_013328345.1_ASM1332834v1_genomic.fna/target_genomes.txt --output GCF_013328345.1_ASM1332834v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:23,658] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:23,659] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgedfe2267-f076-4242-850d-9ca82a832e11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:23,659] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgedfe2267-f076-4242-850d-9ca82a832e11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:23,677] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:23,677] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:23,678] [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
Marinifaba aquimaris	strain=SM1970	GCA_013328345.1	2741323	2741323	type	True	100.0	1353	1356	95	conclusive
Saccharobesus litoralis	strain=CCB-QB4	GCA_003063625.1	2172099	2172099	type	True	78.259	161	1356	95	below_threshold
Algibacillus agarilyticus	strain=RQJ05	GCA_003286125.1	2234133	2234133	type	True	77.9816	144	1356	95	below_threshold
Catenovulum maritimum	strain=Q1	GCA_001050375.1	1513271	1513271	type	True	77.8673	112	1356	95	below_threshold
Catenovulum agarivorans	strain=YM01	GCA_000281085.1	1172192	1172192	type	True	77.6521	128	1356	95	below_threshold
Pseudoalteromonas galatheae	strain=S4498	GCA_005886105.2	579562	579562	type	True	77.3888	66	1356	95	below_threshold
Pseudoalteromonas piscicida	strain=JCM 20779	GCA_000238315.4	43662	43662	type	True	77.2968	69	1356	95	below_threshold
Pseudoalteromonas espejiana	strain=ATCC 29659	GCA_002221525.1	28107	28107	type	True	77.142	74	1356	95	below_threshold
Pseudoalteromonas espejiana	strain=NBRC 102222	GCA_007989585.1	28107	28107	type	True	77.0308	67	1356	95	below_threshold
Alteromonas mediterranea	strain=DE	GCA_000020585.3	314275	314275	type	True	76.9954	60	1356	95	below_threshold
Pseudoalteromonas piscicida	strain=ATCC 15057	GCA_000382005.1	43662	43662	type	True	76.9541	64	1356	95	below_threshold
Shewanella donghaensis	strain=LT17	GCA_007567505.1	238836	238836	type	True	76.8123	64	1356	95	below_threshold
Pseudoalteromonas lipolytica	strain=CGMCC 1.8499	GCA_900116435.1	570156	570156	suspected-type	True	76.7665	80	1356	95	below_threshold
Pseudoalteromonas fuliginea	strain=KMM 216	GCA_000690055.1	1872678	1872678	type	True	76.7493	66	1356	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	76.6749	71	1356	95	below_threshold
Pseudoalteromonas arctica	strain=A 37-1-2	GCA_000238395.4	394751	394751	type	True	76.452	73	1356	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:23,679] [INFO] DFAST Taxonomy check result was written to GCF_013328345.1_ASM1332834v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:23,680] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:23,680] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:23,680] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgedfe2267-f076-4242-850d-9ca82a832e11/dqc_reference/checkm_data
[2024-01-24 13:56:23,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:23,722] [INFO] Task started: CheckM
[2024-01-24 13:56:23,722] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013328345.1_ASM1332834v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013328345.1_ASM1332834v1_genomic.fna/checkm_input GCF_013328345.1_ASM1332834v1_genomic.fna/checkm_result
[2024-01-24 13:56:54,177] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:54,178] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:54,197] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:54,197] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:54,198] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013328345.1_ASM1332834v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:54,198] [INFO] Task started: Blastn
[2024-01-24 13:56:54,199] [INFO] Running command: blastn -query GCF_013328345.1_ASM1332834v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedfe2267-f076-4242-850d-9ca82a832e11/dqc_reference/reference_markers_gtdb.fasta -out GCF_013328345.1_ASM1332834v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:55,300] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:55,304] [INFO] Selected 24 target genomes.
[2024-01-24 13:56:55,304] [INFO] Target genome list was writen to GCF_013328345.1_ASM1332834v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:55,334] [INFO] Task started: fastANI
[2024-01-24 13:56:55,334] [INFO] Running command: fastANI --query /var/lib/cwl/stg97b55ea3-426f-4b23-84fa-09c65f34ccd5/GCF_013328345.1_ASM1332834v1_genomic.fna.gz --refList GCF_013328345.1_ASM1332834v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013328345.1_ASM1332834v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:11,405] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:11,432] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:11,432] [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_013328345.1	s__Marinifaba aquimaris	100.0	1353	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Marinifaba	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003063625.1	s__Algibacillus sp003063625	78.2652	160	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Algibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000568405.1	s__Catenovulum agarivorans_A	78.0061	108	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Catenovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003286125.1	s__Algibacillus agarilyticus	77.986	143	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Algibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050375.1	s__Catenovulum maritimum	77.9252	110	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Catenovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000281085.1	s__Catenovulum agarivorans	77.6308	128	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Catenovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005876835.1	s__Pseudoalteromonas phenolica_B	77.3225	82	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007289895.1	s__Catenovulum sediminis	77.2638	72	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Catenovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004103285.1	s__Pseudoalteromonas sp004103285	77.1973	59	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.27	99.27	0.97	0.97	2	-
GCF_000020585.3	s__Alteromonas mediterranea	77.0767	58	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Alteromonas	95.0	98.15	97.41	0.86	0.82	24	-
GCF_008370255.1	s__Pseudoalteromonas sp008370255	77.0455	60	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019134595.1	s__Pseudoalteromonas shioyasakiensis_A	76.9646	105	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.6918	N/A	N/A	N/A	N/A	1	-
GCF_003675895.1	s__Parashewanella curva	76.9579	52	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007567505.1	s__Shewanella donghaensis	76.8448	63	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000690055.1	s__Pseudoalteromonas fuliginea	76.784	66	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.33	97.88	0.92	0.87	9	-
GCF_000239855.1	s__Pseudoalteromonas sp000239855	76.6104	61	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000238395.3	s__Pseudoalteromonas arctica	76.4922	70	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.91	96.03	0.87	0.80	33	-
GCF_001974875.1	s__Pseudoalteromonas sp001974875	76.4224	73	1356	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.73	97.18	0.90	0.86	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:11,434] [INFO] GTDB search result was written to GCF_013328345.1_ASM1332834v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:11,435] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:11,441] [INFO] DFAST_QC result json was written to GCF_013328345.1_ASM1332834v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:11,442] [INFO] DFAST_QC completed!
[2024-01-24 13:57:11,442] [INFO] Total running time: 0h1m13s