[2024-01-24 12:28:34,760] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:28:34,762] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:28:34,762] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f8c4cab-0ebe-4dc7-aba3-cb2a19e0befd/dqc_reference
[2024-01-24 12:28:35,964] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:28:35,965] [INFO] Task started: Prodigal
[2024-01-24 12:28:35,965] [INFO] Running command: gunzip -c /var/lib/cwl/stg899c9484-41e4-41c2-8500-e30ab45df2e0/GCF_007197755.1_ASM719775v1_genomic.fna.gz | prodigal -d GCF_007197755.1_ASM719775v1_genomic.fna/cds.fna -a GCF_007197755.1_ASM719775v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:28:48,973] [INFO] Task succeeded: Prodigal
[2024-01-24 12:28:48,974] [INFO] Task started: HMMsearch
[2024-01-24 12:28:48,974] [INFO] Running command: hmmsearch --tblout GCF_007197755.1_ASM719775v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f8c4cab-0ebe-4dc7-aba3-cb2a19e0befd/dqc_reference/reference_markers.hmm GCF_007197755.1_ASM719775v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:28:49,258] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:28:49,260] [INFO] Found 6/6 markers.
[2024-01-24 12:28:49,302] [INFO] Query marker FASTA was written to GCF_007197755.1_ASM719775v1_genomic.fna/markers.fasta
[2024-01-24 12:28:49,303] [INFO] Task started: Blastn
[2024-01-24 12:28:49,303] [INFO] Running command: blastn -query GCF_007197755.1_ASM719775v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f8c4cab-0ebe-4dc7-aba3-cb2a19e0befd/dqc_reference/reference_markers.fasta -out GCF_007197755.1_ASM719775v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:28:50,288] [INFO] Task succeeded: Blastn
[2024-01-24 12:28:50,292] [INFO] Selected 27 target genomes.
[2024-01-24 12:28:50,293] [INFO] Target genome list was writen to GCF_007197755.1_ASM719775v1_genomic.fna/target_genomes.txt
[2024-01-24 12:28:50,323] [INFO] Task started: fastANI
[2024-01-24 12:28:50,323] [INFO] Running command: fastANI --query /var/lib/cwl/stg899c9484-41e4-41c2-8500-e30ab45df2e0/GCF_007197755.1_ASM719775v1_genomic.fna.gz --refList GCF_007197755.1_ASM719775v1_genomic.fna/target_genomes.txt --output GCF_007197755.1_ASM719775v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:13,823] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:13,824] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f8c4cab-0ebe-4dc7-aba3-cb2a19e0befd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:13,824] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f8c4cab-0ebe-4dc7-aba3-cb2a19e0befd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:13,855] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:29:13,855] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:13,856] [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
Ferrovibrio terrae	strain=K5	GCA_007197755.1	2594003	2594003	type	True	100.0	1421	1421	95	conclusive
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	77.2727	270	1421	95	below_threshold
Azospirillum thiophilum	strain=BV-S	GCA_001305595.1	528244	528244	type	True	77.2054	316	1421	95	below_threshold
Azospirillum humicireducens	strain=SgZ-5	GCA_001639105.2	1226968	1226968	type	True	77.1481	312	1421	95	below_threshold
Azospirillum ramasamyi	strain=M2T2B2	GCA_003233655.1	682998	682998	type	True	77.123	295	1421	95	below_threshold
Azospirillum thiophilum	strain=DSM 21654	GCA_000960825.1	528244	528244	type	True	77.1219	325	1421	95	below_threshold
Reyranella massiliensis	strain=521	GCA_000312425.1	445220	445220	type	True	77.0768	269	1421	95	below_threshold
Azospirillum melinis	strain=TMCY0552	GCA_013340935.1	328839	328839	type	True	77.0763	309	1421	95	below_threshold
Azospirillum melinis	strain=TMCY 0552	GCA_017876055.1	328839	328839	type	True	76.9994	318	1421	95	below_threshold
Azospirillum oryzae	strain=COC8	GCA_008364795.1	286727	286727	type	True	76.9963	306	1421	95	below_threshold
Azorhizobium caulinodans	strain=ORS 571	GCA_000010525.1	7	7	type	True	76.8451	206	1421	95	below_threshold
Minwuia thermotolerans	strain=SY3-15	GCA_002924445.1	2056226	2056226	type	True	76.8038	245	1421	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	76.7847	364	1421	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	76.7404	379	1421	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.6169	271	1421	95	below_threshold
Bosea psychrotolerans	strain=1131	GCA_002917105.1	1871628	1871628	type	True	76.601	255	1421	95	below_threshold
Pararhodospirillum photometricum	strain=DSM 122	GCA_000284415.2	1084	1084	type	True	76.5866	97	1421	95	below_threshold
Rhodoplanes piscinae	strain=DSM 19946	GCA_003258855.1	444923	444923	type	True	76.4697	215	1421	95	below_threshold
Euryhalocaulis caribicus	strain=JL2009	GCA_000412185.1	1161401	1161401	type	True	76.4696	109	1421	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	76.4662	229	1421	95	below_threshold
Microvirga thermotolerans	strain=HR1	GCA_009363855.1	2651334	2651334	type	True	76.4157	137	1421	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	76.4141	152	1421	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	76.3778	133	1421	95	below_threshold
Roseococcus microcysteis	strain=NIBR12	GCA_014764365.1	2771361	2771361	type	True	76.3587	174	1421	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.338	253	1421	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	76.29	167	1421	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.1015	132	1421	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:13,858] [INFO] DFAST Taxonomy check result was written to GCF_007197755.1_ASM719775v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:13,858] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:13,858] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:13,859] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f8c4cab-0ebe-4dc7-aba3-cb2a19e0befd/dqc_reference/checkm_data
[2024-01-24 12:29:13,859] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:13,898] [INFO] Task started: CheckM
[2024-01-24 12:29:13,899] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007197755.1_ASM719775v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007197755.1_ASM719775v1_genomic.fna/checkm_input GCF_007197755.1_ASM719775v1_genomic.fna/checkm_result
[2024-01-24 12:29:54,929] [INFO] Task succeeded: CheckM
[2024-01-24 12:29:54,930] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:29:54,952] [INFO] ===== Completeness check finished =====
[2024-01-24 12:29:54,953] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:29:54,953] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007197755.1_ASM719775v1_genomic.fna/markers.fasta)
[2024-01-24 12:29:54,954] [INFO] Task started: Blastn
[2024-01-24 12:29:54,954] [INFO] Running command: blastn -query GCF_007197755.1_ASM719775v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f8c4cab-0ebe-4dc7-aba3-cb2a19e0befd/dqc_reference/reference_markers_gtdb.fasta -out GCF_007197755.1_ASM719775v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:56,928] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:56,933] [INFO] Selected 8 target genomes.
[2024-01-24 12:29:56,933] [INFO] Target genome list was writen to GCF_007197755.1_ASM719775v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:29:56,944] [INFO] Task started: fastANI
[2024-01-24 12:29:56,945] [INFO] Running command: fastANI --query /var/lib/cwl/stg899c9484-41e4-41c2-8500-e30ab45df2e0/GCF_007197755.1_ASM719775v1_genomic.fna.gz --refList GCF_007197755.1_ASM719775v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007197755.1_ASM719775v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:04,808] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:04,820] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:04,821] [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_007197755.1	s__Ferrovibrio terrae	100.0	1421	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018336035.1	s__Ferrovibrio sp018336035	89.3158	1133	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002796975.1	s__Ferrovibrio sp002796975	88.2467	1175	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017991315.1	s__Ferrovibrio sp017991315	80.5462	491	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482765.1	s__Ferrovibrio sp002482765	79.7467	631	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__Ferrovibrio	95.0	95.40	95.40	0.86	0.86	2	-
GCA_017307375.1	s__JAFKFH01 sp017307375	77.7495	465	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Ferrovibrionales;f__Ferrovibrionaceae;g__JAFKFH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010032545.1	s__Reyranella sp010032545	76.7931	207	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Reyranellales;f__Reyranellaceae;g__Reyranella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013003675.1	s__JABDIP01 sp013003675	76.5441	173	1421	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__JABDIP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:04,822] [INFO] GTDB search result was written to GCF_007197755.1_ASM719775v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:04,823] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:04,827] [INFO] DFAST_QC result json was written to GCF_007197755.1_ASM719775v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:04,827] [INFO] DFAST_QC completed!
[2024-01-24 12:30:04,828] [INFO] Total running time: 0h1m30s