[2024-01-24 14:12:47,088] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:47,090] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:47,090] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e7ea6ff-5cd5-46d5-b820-b2504e262c6b/dqc_reference
[2024-01-24 14:12:48,325] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:48,326] [INFO] Task started: Prodigal
[2024-01-24 14:12:48,326] [INFO] Running command: gunzip -c /var/lib/cwl/stg77cc4bfa-25fc-4499-b57c-a74279852cde/GCF_001618175.1_ASM161817v1_genomic.fna.gz | prodigal -d GCF_001618175.1_ASM161817v1_genomic.fna/cds.fna -a GCF_001618175.1_ASM161817v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:58,924] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:58,925] [INFO] Task started: HMMsearch
[2024-01-24 14:12:58,925] [INFO] Running command: hmmsearch --tblout GCF_001618175.1_ASM161817v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e7ea6ff-5cd5-46d5-b820-b2504e262c6b/dqc_reference/reference_markers.hmm GCF_001618175.1_ASM161817v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:59,201] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:59,203] [INFO] Found 6/6 markers.
[2024-01-24 14:12:59,249] [INFO] Query marker FASTA was written to GCF_001618175.1_ASM161817v1_genomic.fna/markers.fasta
[2024-01-24 14:12:59,249] [INFO] Task started: Blastn
[2024-01-24 14:12:59,249] [INFO] Running command: blastn -query GCF_001618175.1_ASM161817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e7ea6ff-5cd5-46d5-b820-b2504e262c6b/dqc_reference/reference_markers.fasta -out GCF_001618175.1_ASM161817v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:00,273] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:00,277] [INFO] Selected 18 target genomes.
[2024-01-24 14:13:00,277] [INFO] Target genome list was writen to GCF_001618175.1_ASM161817v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:00,285] [INFO] Task started: fastANI
[2024-01-24 14:13:00,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg77cc4bfa-25fc-4499-b57c-a74279852cde/GCF_001618175.1_ASM161817v1_genomic.fna.gz --refList GCF_001618175.1_ASM161817v1_genomic.fna/target_genomes.txt --output GCF_001618175.1_ASM161817v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:16,638] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:16,639] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e7ea6ff-5cd5-46d5-b820-b2504e262c6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:16,639] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e7ea6ff-5cd5-46d5-b820-b2504e262c6b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:16,657] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:16,657] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:16,657] [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
Oceanibaculum pacificum	strain=MCCC 1A02656	GCA_001618175.1	580166	580166	type	True	100.0	1194	1204	95	conclusive
Oceanibaculum nanhaiense	strain=L54-1-50	GCA_002148795.1	1909734	1909734	type	True	83.9918	777	1204	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	83.898	757	1204	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	77.5326	388	1204	95	below_threshold
Magnetospirillum moscoviense	strain=BB-1	GCA_001650635.1	1437059	1437059	type	True	77.4748	267	1204	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	77.4671	251	1204	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	77.4229	395	1204	95	below_threshold
Azospirillum tabaci	strain=W712	GCA_014596085.1	2752310	2752310	type	True	77.3896	394	1204	95	below_threshold
Azospirillum formosense	strain=CC-NFb-7	GCA_013340925.1	861533	861533	type	True	77.3758	355	1204	95	below_threshold
Azospirillum argentinense	strain=Az39	GCA_000632475.2	2970906	2970906	type	True	77.3698	412	1204	95	below_threshold
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	77.268	378	1204	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	77.2574	382	1204	95	below_threshold
Rhodospirillum rubrum	strain=DSM 467	GCA_019134555.1	1085	1085	type	True	77.0097	208	1204	95	below_threshold
Reyranella aquatilis	strain=KCTC 52223	GCA_020880995.1	2035356	2035356	type	True	76.9579	257	1204	95	below_threshold
Niveispirillum cyanobacteriorum	strain=CGMCC 1.12958	GCA_014640215.1	1612173	1612173	type	True	76.6518	221	1204	95	below_threshold
Shinella pollutisoli	strain=KCTC 52677	GCA_024609765.1	2250594	2250594	type	True	76.5819	214	1204	95	below_threshold
Methylobacterium dankookense	strain=DSM 22415	GCA_022179165.1	560405	560405	type	True	76.4355	214	1204	95	below_threshold
Roseococcus pinisoli	strain=XZZS9	GCA_018413645.1	2835040	2835040	type	True	76.3422	238	1204	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:16,661] [INFO] DFAST Taxonomy check result was written to GCF_001618175.1_ASM161817v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:16,661] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:16,662] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:16,662] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e7ea6ff-5cd5-46d5-b820-b2504e262c6b/dqc_reference/checkm_data
[2024-01-24 14:13:16,663] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:16,700] [INFO] Task started: CheckM
[2024-01-24 14:13:16,701] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001618175.1_ASM161817v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001618175.1_ASM161817v1_genomic.fna/checkm_input GCF_001618175.1_ASM161817v1_genomic.fna/checkm_result
[2024-01-24 14:13:50,647] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:50,648] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:50,666] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:50,667] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:50,667] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001618175.1_ASM161817v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:50,667] [INFO] Task started: Blastn
[2024-01-24 14:13:50,668] [INFO] Running command: blastn -query GCF_001618175.1_ASM161817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e7ea6ff-5cd5-46d5-b820-b2504e262c6b/dqc_reference/reference_markers_gtdb.fasta -out GCF_001618175.1_ASM161817v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:52,706] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:52,710] [INFO] Selected 11 target genomes.
[2024-01-24 14:13:52,710] [INFO] Target genome list was writen to GCF_001618175.1_ASM161817v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:52,719] [INFO] Task started: fastANI
[2024-01-24 14:13:52,719] [INFO] Running command: fastANI --query /var/lib/cwl/stg77cc4bfa-25fc-4499-b57c-a74279852cde/GCF_001618175.1_ASM161817v1_genomic.fna.gz --refList GCF_001618175.1_ASM161817v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001618175.1_ASM161817v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:03,706] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:03,717] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:03,718] [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_001618175.1	s__Oceanibaculum pacificum	100.0	1194	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018823745.1	s__Oceanibaculum sp018823745	86.0515	896	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	99.98	99.98	1.00	1.00	4	-
GCF_002148795.1	s__Oceanibaculum nanhaiense	83.9967	774	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000299935.1	s__Oceanibaculum indicum	83.8674	760	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Oceanibaculales;f__Oceanibaculaceae;g__Oceanibaculum	95.0	97.37	97.37	0.93	0.93	2	-
GCA_006739055.1	s__Stella vacuolata	77.6318	412	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__ATCC43930;f__Stellaceae;g__Stella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	77.5331	388	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003349955.1	s__Azospirillum brasilense_B	77.3524	423	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	95.36	95.36	0.89	0.89	2	-
GCF_008365375.1	s__Azospirillum sp008365375	77.2265	373	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869645.1	s__SHVW01 sp016869645	77.1628	280	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVW01;f__SHVW01;g__SHVW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009694025.1	s__SHVZ01 sp009694025	76.8971	205	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__SHVZ01;f__SHVZ01;g__SHVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014359905.1	s__Hoeflea sp014359905	76.7592	180	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__Hoeflea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:03,721] [INFO] GTDB search result was written to GCF_001618175.1_ASM161817v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:03,722] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:03,728] [INFO] DFAST_QC result json was written to GCF_001618175.1_ASM161817v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:03,729] [INFO] DFAST_QC completed!
[2024-01-24 14:14:03,729] [INFO] Total running time: 0h1m17s