[2024-01-25 18:28:50,789] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:28:50,791] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:28:50,791] [INFO] DQC Reference Directory: /var/lib/cwl/stgd0226695-5d17-4562-97cc-dc55d92c5134/dqc_reference
[2024-01-25 18:28:51,911] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:28:51,912] [INFO] Task started: Prodigal
[2024-01-25 18:28:51,912] [INFO] Running command: gunzip -c /var/lib/cwl/stg208a57b5-2a4c-4ce7-bd60-43dc9ace2e98/GCF_002020355.1_ASM202035v1_genomic.fna.gz | prodigal -d GCF_002020355.1_ASM202035v1_genomic.fna/cds.fna -a GCF_002020355.1_ASM202035v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:29:02,973] [INFO] Task succeeded: Prodigal
[2024-01-25 18:29:02,974] [INFO] Task started: HMMsearch
[2024-01-25 18:29:02,974] [INFO] Running command: hmmsearch --tblout GCF_002020355.1_ASM202035v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd0226695-5d17-4562-97cc-dc55d92c5134/dqc_reference/reference_markers.hmm GCF_002020355.1_ASM202035v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:29:03,205] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:29:03,206] [INFO] Found 6/6 markers.
[2024-01-25 18:29:03,245] [INFO] Query marker FASTA was written to GCF_002020355.1_ASM202035v1_genomic.fna/markers.fasta
[2024-01-25 18:29:03,246] [INFO] Task started: Blastn
[2024-01-25 18:29:03,246] [INFO] Running command: blastn -query GCF_002020355.1_ASM202035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0226695-5d17-4562-97cc-dc55d92c5134/dqc_reference/reference_markers.fasta -out GCF_002020355.1_ASM202035v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:29:04,141] [INFO] Task succeeded: Blastn
[2024-01-25 18:29:04,144] [INFO] Selected 11 target genomes.
[2024-01-25 18:29:04,144] [INFO] Target genome list was writen to GCF_002020355.1_ASM202035v1_genomic.fna/target_genomes.txt
[2024-01-25 18:29:04,148] [INFO] Task started: fastANI
[2024-01-25 18:29:04,148] [INFO] Running command: fastANI --query /var/lib/cwl/stg208a57b5-2a4c-4ce7-bd60-43dc9ace2e98/GCF_002020355.1_ASM202035v1_genomic.fna.gz --refList GCF_002020355.1_ASM202035v1_genomic.fna/target_genomes.txt --output GCF_002020355.1_ASM202035v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:29:13,970] [INFO] Task succeeded: fastANI
[2024-01-25 18:29:13,971] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd0226695-5d17-4562-97cc-dc55d92c5134/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:29:13,971] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd0226695-5d17-4562-97cc-dc55d92c5134/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:29:13,979] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:29:13,979] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:29:13,979] [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
Thioclava sediminum	strain=TAW-CT134	GCA_002020355.1	1915319	1915319	type	True	100.0	1373	1373	95	inconclusive
Thioclava electrotropha	strain=Elox9	GCA_002085925.2	1549850	1549850	type	True	96.2561	1262	1373	95	inconclusive
Thioclava nitratireducens	strain=25B10_4	GCA_001940525.2	1915078	1915078	type	True	91.6127	1125	1373	95	below_threshold
Thioclava pacifica	strain=DSM 10166	GCA_000714535.1	285109	285109	type	True	85.1817	910	1373	95	below_threshold
Thioclava marina	strain=11.10-0-13	GCA_002020135.1	1915077	1915077	type	True	85.0516	916	1373	95	below_threshold
Thioclava atlantica	strain=13D2W-2	GCA_000737065.1	1317124	1317124	type	True	84.2654	898	1373	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	78.0792	346	1373	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	77.7772	364	1373	95	below_threshold
Halovulum dunhuangense	strain=YYQ-30	GCA_013093415.1	1505036	1505036	type	True	77.7155	349	1373	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	77.3419	299	1373	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	77.3111	344	1373	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:29:13,980] [INFO] DFAST Taxonomy check result was written to GCF_002020355.1_ASM202035v1_genomic.fna/tc_result.tsv
[2024-01-25 18:29:13,981] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:29:13,981] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:29:13,981] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd0226695-5d17-4562-97cc-dc55d92c5134/dqc_reference/checkm_data
[2024-01-25 18:29:13,982] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:29:14,024] [INFO] Task started: CheckM
[2024-01-25 18:29:14,024] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002020355.1_ASM202035v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002020355.1_ASM202035v1_genomic.fna/checkm_input GCF_002020355.1_ASM202035v1_genomic.fna/checkm_result
[2024-01-25 18:29:48,120] [INFO] Task succeeded: CheckM
[2024-01-25 18:29:48,124] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:29:48,143] [INFO] ===== Completeness check finished =====
[2024-01-25 18:29:48,143] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:29:48,144] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002020355.1_ASM202035v1_genomic.fna/markers.fasta)
[2024-01-25 18:29:48,144] [INFO] Task started: Blastn
[2024-01-25 18:29:48,144] [INFO] Running command: blastn -query GCF_002020355.1_ASM202035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd0226695-5d17-4562-97cc-dc55d92c5134/dqc_reference/reference_markers_gtdb.fasta -out GCF_002020355.1_ASM202035v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:29:49,991] [INFO] Task succeeded: Blastn
[2024-01-25 18:29:49,993] [INFO] Selected 5 target genomes.
[2024-01-25 18:29:49,994] [INFO] Target genome list was writen to GCF_002020355.1_ASM202035v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:29:49,999] [INFO] Task started: fastANI
[2024-01-25 18:29:50,000] [INFO] Running command: fastANI --query /var/lib/cwl/stg208a57b5-2a4c-4ce7-bd60-43dc9ace2e98/GCF_002020355.1_ASM202035v1_genomic.fna.gz --refList GCF_002020355.1_ASM202035v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002020355.1_ASM202035v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:29:55,619] [INFO] Task succeeded: fastANI
[2024-01-25 18:29:55,624] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:29:55,624] [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_002020355.1	s__Thioclava sediminum	100.0	1373	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2561	96.53	96.29	0.92	0.90	8	conclusive
GCF_002085925.2	s__Thioclava electrotropha	96.2561	1262	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2561	N/A	N/A	N/A	N/A	1	conclusive
GCF_009296265.1	s__Thioclava sp009296265	96.2206	1250	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	96.2474	N/A	N/A	N/A	N/A	1	-
GCF_002563775.1	s__Thioclava sp002563775	95.0268	1137	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0406	95.45	95.45	0.86	0.86	2	-
GCF_001940525.2	s__Thioclava nitratireducens	91.6127	1125	1373	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thioclava	95.0	98.60	98.50	0.92	0.89	7	-
--------------------------------------------------------------------------------
[2024-01-25 18:29:55,625] [INFO] GTDB search result was written to GCF_002020355.1_ASM202035v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:29:55,626] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:29:55,628] [INFO] DFAST_QC result json was written to GCF_002020355.1_ASM202035v1_genomic.fna/dqc_result.json
[2024-01-25 18:29:55,628] [INFO] DFAST_QC completed!
[2024-01-25 18:29:55,628] [INFO] Total running time: 0h1m5s