[2024-01-24 12:53:49,413] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:49,416] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:49,416] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ec871c0-9cfe-411f-b1cd-d13222d6922d/dqc_reference
[2024-01-24 12:53:51,729] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:51,730] [INFO] Task started: Prodigal
[2024-01-24 12:53:51,730] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf8f89cd-7bd3-43de-96bc-a1f0279cd671/GCF_025532145.1_ASM2553214v1_genomic.fna.gz | prodigal -d GCF_025532145.1_ASM2553214v1_genomic.fna/cds.fna -a GCF_025532145.1_ASM2553214v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:06,326] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:06,327] [INFO] Task started: HMMsearch
[2024-01-24 12:54:06,327] [INFO] Running command: hmmsearch --tblout GCF_025532145.1_ASM2553214v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ec871c0-9cfe-411f-b1cd-d13222d6922d/dqc_reference/reference_markers.hmm GCF_025532145.1_ASM2553214v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:06,629] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:06,630] [INFO] Found 6/6 markers.
[2024-01-24 12:54:06,676] [INFO] Query marker FASTA was written to GCF_025532145.1_ASM2553214v1_genomic.fna/markers.fasta
[2024-01-24 12:54:06,676] [INFO] Task started: Blastn
[2024-01-24 12:54:06,676] [INFO] Running command: blastn -query GCF_025532145.1_ASM2553214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ec871c0-9cfe-411f-b1cd-d13222d6922d/dqc_reference/reference_markers.fasta -out GCF_025532145.1_ASM2553214v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:07,566] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:07,572] [INFO] Selected 10 target genomes.
[2024-01-24 12:54:07,572] [INFO] Target genome list was writen to GCF_025532145.1_ASM2553214v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:07,582] [INFO] Task started: fastANI
[2024-01-24 12:54:07,583] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf8f89cd-7bd3-43de-96bc-a1f0279cd671/GCF_025532145.1_ASM2553214v1_genomic.fna.gz --refList GCF_025532145.1_ASM2553214v1_genomic.fna/target_genomes.txt --output GCF_025532145.1_ASM2553214v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:17,236] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:17,237] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ec871c0-9cfe-411f-b1cd-d13222d6922d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:17,237] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ec871c0-9cfe-411f-b1cd-d13222d6922d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:17,251] [INFO] Found 10 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:54:17,252] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:54:17,252] [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
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	100.0	1534	1536	95	inconclusive
Alcanivorax dieselolei	strain=CGMCC 1.3690	GCA_014644575.1	285091	285091	type	True	95.1259	1369	1536	95	inconclusive
Alcanivorax dieselolei	strain=B5	GCA_000300005.1	285091	285091	type	True	95.1034	1371	1536	95	inconclusive
Alcanivorax xenomutans	strain=JC109	GCA_900217905.1	1094342	1094342	type	True	94.5605	1293	1536	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	80.8932	647	1536	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	80.6456	752	1536	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	80.4904	733	1536	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	77.8166	244	1536	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	77.0806	151	1536	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	77.0742	152	1536	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:17,253] [INFO] DFAST Taxonomy check result was written to GCF_025532145.1_ASM2553214v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:17,254] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:17,254] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:17,254] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ec871c0-9cfe-411f-b1cd-d13222d6922d/dqc_reference/checkm_data
[2024-01-24 12:54:17,256] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:17,311] [INFO] Task started: CheckM
[2024-01-24 12:54:17,312] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025532145.1_ASM2553214v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025532145.1_ASM2553214v1_genomic.fna/checkm_input GCF_025532145.1_ASM2553214v1_genomic.fna/checkm_result
[2024-01-24 12:55:01,667] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:01,668] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:01,704] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:01,705] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:01,706] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025532145.1_ASM2553214v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:01,706] [INFO] Task started: Blastn
[2024-01-24 12:55:01,706] [INFO] Running command: blastn -query GCF_025532145.1_ASM2553214v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ec871c0-9cfe-411f-b1cd-d13222d6922d/dqc_reference/reference_markers_gtdb.fasta -out GCF_025532145.1_ASM2553214v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:03,331] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:03,335] [INFO] Selected 11 target genomes.
[2024-01-24 12:55:03,335] [INFO] Target genome list was writen to GCF_025532145.1_ASM2553214v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:03,387] [INFO] Task started: fastANI
[2024-01-24 12:55:03,387] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf8f89cd-7bd3-43de-96bc-a1f0279cd671/GCF_025532145.1_ASM2553214v1_genomic.fna.gz --refList GCF_025532145.1_ASM2553214v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025532145.1_ASM2553214v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:13,547] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:13,558] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:13,559] [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_000300005.1	s__Alcanivorax dieselolei	95.0883	1372	1536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.56	95.12	0.92	0.84	3	conclusive
GCF_900217905.1	s__Alcanivorax xenomutans	94.5565	1294	1536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.43	98.18	0.92	0.84	9	-
GCF_004360225.1	s__Alcanivorax sp004360225	90.6671	1296	1536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.14	99.14	0.91	0.91	2	-
GCF_016906305.1	s__Alcanivorax marinus_B	80.8004	723	1536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015265435.1	s__Alcanivorax profundimaris	80.6448	752	1536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.49	97.23	0.85	0.77	11	-
GCF_005938655.1	s__Alcanivorax gelatiniphagus	80.507	731	1536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.53	98.53	0.93	0.93	3	-
GCF_015356855.1	s__Alcanivorax venustensis	80.4913	651	1536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.73	95.38	0.91	0.87	46	-
GCF_016785095.1	s__Alcanivorax marinus_A	80.2893	709	1536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002389055.1	s__Alcanivorax sp002389055	79.8709	541	1536	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	96.98	96.27	0.78	0.74	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:13,560] [INFO] GTDB search result was written to GCF_025532145.1_ASM2553214v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:13,561] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:13,565] [INFO] DFAST_QC result json was written to GCF_025532145.1_ASM2553214v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:13,565] [INFO] DFAST_QC completed!
[2024-01-24 12:55:13,565] [INFO] Total running time: 0h1m24s