[2024-01-24 13:58:10,332] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,334] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,334] [INFO] DQC Reference Directory: /var/lib/cwl/stg72534261-cd39-4027-b6e2-5a0e5a540a17/dqc_reference
[2024-01-24 13:58:11,697] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:11,700] [INFO] Task started: Prodigal
[2024-01-24 13:58:11,701] [INFO] Running command: gunzip -c /var/lib/cwl/stg685742d0-7f9b-484b-b9a0-0c7b288b9a91/GCF_009601165.1_ASM960116v1_genomic.fna.gz | prodigal -d GCF_009601165.1_ASM960116v1_genomic.fna/cds.fna -a GCF_009601165.1_ASM960116v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:23,600] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:23,601] [INFO] Task started: HMMsearch
[2024-01-24 13:58:23,601] [INFO] Running command: hmmsearch --tblout GCF_009601165.1_ASM960116v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72534261-cd39-4027-b6e2-5a0e5a540a17/dqc_reference/reference_markers.hmm GCF_009601165.1_ASM960116v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:23,874] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:23,875] [INFO] Found 6/6 markers.
[2024-01-24 13:58:23,918] [INFO] Query marker FASTA was written to GCF_009601165.1_ASM960116v1_genomic.fna/markers.fasta
[2024-01-24 13:58:23,919] [INFO] Task started: Blastn
[2024-01-24 13:58:23,919] [INFO] Running command: blastn -query GCF_009601165.1_ASM960116v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72534261-cd39-4027-b6e2-5a0e5a540a17/dqc_reference/reference_markers.fasta -out GCF_009601165.1_ASM960116v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:24,761] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:24,766] [INFO] Selected 12 target genomes.
[2024-01-24 13:58:24,767] [INFO] Target genome list was writen to GCF_009601165.1_ASM960116v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:24,772] [INFO] Task started: fastANI
[2024-01-24 13:58:24,772] [INFO] Running command: fastANI --query /var/lib/cwl/stg685742d0-7f9b-484b-b9a0-0c7b288b9a91/GCF_009601165.1_ASM960116v1_genomic.fna.gz --refList GCF_009601165.1_ASM960116v1_genomic.fna/target_genomes.txt --output GCF_009601165.1_ASM960116v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:33,986] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:33,987] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72534261-cd39-4027-b6e2-5a0e5a540a17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:33,987] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72534261-cd39-4027-b6e2-5a0e5a540a17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:34,000] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:34,000] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:34,000] [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 sediminis	strain=PA15-N-34	GCA_009601165.1	2663008	2663008	type	True	100.0	1264	1264	95	conclusive
Alcanivorax nanhaiticus	strain=19-m-6	GCA_000756665.1	1177154	1177154	type	True	83.8179	894	1264	95	below_threshold
Alcanivorax profundi	strain=MTEO17	GCA_003597125.1	2338368	2338368	type	True	81.853	679	1264	95	below_threshold
Alcanivorax jadensis	strain=T9	GCA_000756655.1	64988	64988	type	True	80.7939	664	1264	95	below_threshold
Alcanivorax hongdengensis	strain=A-11-3	GCA_000300995.1	519051	519051	type	True	80.4815	593	1264	95	below_threshold
Alcanivorax borkumensis	strain=SK2	GCA_000009365.1	59754	59754	type	True	79.2572	430	1264	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	78.6645	355	1264	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	78.5987	337	1264	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	78.2305	322	1264	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	77.8482	220	1264	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:34,002] [INFO] DFAST Taxonomy check result was written to GCF_009601165.1_ASM960116v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:34,003] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:34,003] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:34,003] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72534261-cd39-4027-b6e2-5a0e5a540a17/dqc_reference/checkm_data
[2024-01-24 13:58:34,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:34,040] [INFO] Task started: CheckM
[2024-01-24 13:58:34,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009601165.1_ASM960116v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009601165.1_ASM960116v1_genomic.fna/checkm_input GCF_009601165.1_ASM960116v1_genomic.fna/checkm_result
[2024-01-24 13:59:12,574] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:12,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:12,595] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:12,595] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:12,596] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009601165.1_ASM960116v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:12,596] [INFO] Task started: Blastn
[2024-01-24 13:59:12,597] [INFO] Running command: blastn -query GCF_009601165.1_ASM960116v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72534261-cd39-4027-b6e2-5a0e5a540a17/dqc_reference/reference_markers_gtdb.fasta -out GCF_009601165.1_ASM960116v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:13,937] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:13,942] [INFO] Selected 11 target genomes.
[2024-01-24 13:59:13,942] [INFO] Target genome list was writen to GCF_009601165.1_ASM960116v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:13,955] [INFO] Task started: fastANI
[2024-01-24 13:59:13,955] [INFO] Running command: fastANI --query /var/lib/cwl/stg685742d0-7f9b-484b-b9a0-0c7b288b9a91/GCF_009601165.1_ASM960116v1_genomic.fna.gz --refList GCF_009601165.1_ASM960116v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009601165.1_ASM960116v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:23,998] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:24,012] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:24,012] [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_009601165.1	s__Alcanivorax sediminis	100.0	1264	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000756665.1	s__Alcanivorax nanhaiticus	83.8127	895	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009882945.1	s__Alcanivorax sp009882945	83.4553	906	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017794965.1	s__Alcanivorax sp017794965	83.4125	909	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003597125.1	s__Alcanivorax profundi	81.8575	679	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.31	99.31	0.96	0.96	2	-
GCA_002706085.1	s__Alcanivorax sp002706085	81.7056	673	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.88	97.88	0.86	0.86	2	-
GCA_003862375.1	s__Alcanivorax jadensis_A	80.9739	670	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.67	99.67	0.92	0.92	2	-
GCF_000756655.1	s__Alcanivorax jadensis	80.8035	663	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.11	97.73	0.92	0.86	7	-
GCF_900107995.1	s__Alcanivorax sp900107995	80.7571	689	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.42	98.03	0.93	0.89	9	-
GCF_000155615.1	s__Alcanivorax sp000155615	80.7214	661	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.88	97.69	0.92	0.89	4	-
GCF_000300995.1	s__Alcanivorax hongdengensis	80.4616	595	1264	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:24,014] [INFO] GTDB search result was written to GCF_009601165.1_ASM960116v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:24,015] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:24,018] [INFO] DFAST_QC result json was written to GCF_009601165.1_ASM960116v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:24,018] [INFO] DFAST_QC completed!
[2024-01-24 13:59:24,018] [INFO] Total running time: 0h1m14s