[2024-01-24 13:36:43,389] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:43,400] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:43,400] [INFO] DQC Reference Directory: /var/lib/cwl/stgf407e9b0-458e-426a-bac8-28e2afacde2d/dqc_reference
[2024-01-24 13:36:44,648] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:44,649] [INFO] Task started: Prodigal
[2024-01-24 13:36:44,650] [INFO] Running command: gunzip -c /var/lib/cwl/stgd25eff42-5794-48eb-a0f4-2505e8d6a986/GCF_014202905.1_ASM1420290v1_genomic.fna.gz | prodigal -d GCF_014202905.1_ASM1420290v1_genomic.fna/cds.fna -a GCF_014202905.1_ASM1420290v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:36:59,442] [INFO] Task succeeded: Prodigal
[2024-01-24 13:36:59,442] [INFO] Task started: HMMsearch
[2024-01-24 13:36:59,442] [INFO] Running command: hmmsearch --tblout GCF_014202905.1_ASM1420290v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf407e9b0-458e-426a-bac8-28e2afacde2d/dqc_reference/reference_markers.hmm GCF_014202905.1_ASM1420290v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:36:59,693] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:36:59,695] [INFO] Found 6/6 markers.
[2024-01-24 13:36:59,730] [INFO] Query marker FASTA was written to GCF_014202905.1_ASM1420290v1_genomic.fna/markers.fasta
[2024-01-24 13:36:59,730] [INFO] Task started: Blastn
[2024-01-24 13:36:59,731] [INFO] Running command: blastn -query GCF_014202905.1_ASM1420290v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf407e9b0-458e-426a-bac8-28e2afacde2d/dqc_reference/reference_markers.fasta -out GCF_014202905.1_ASM1420290v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:00,532] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:00,535] [INFO] Selected 29 target genomes.
[2024-01-24 13:37:00,535] [INFO] Target genome list was writen to GCF_014202905.1_ASM1420290v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:00,546] [INFO] Task started: fastANI
[2024-01-24 13:37:00,546] [INFO] Running command: fastANI --query /var/lib/cwl/stgd25eff42-5794-48eb-a0f4-2505e8d6a986/GCF_014202905.1_ASM1420290v1_genomic.fna.gz --refList GCF_014202905.1_ASM1420290v1_genomic.fna/target_genomes.txt --output GCF_014202905.1_ASM1420290v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:19,246] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:19,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf407e9b0-458e-426a-bac8-28e2afacde2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:19,247] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf407e9b0-458e-426a-bac8-28e2afacde2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:19,258] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:19,258] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:19,258] [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
Chitinivorax tropicus	strain=DSM 27165	GCA_014202905.1	714531	714531	type	True	100.0	1418	1423	95	conclusive
Andreprevotia chitinilytica	strain=DSM 18519	GCA_000711875.1	396808	396808	type	True	76.6157	89	1423	95	below_threshold
Aquitalea magnusonii	strain=DSM 25134	GCA_003202035.1	332411	332411	suspected-type	True	76.4967	110	1423	95	below_threshold
Chitinilyticum piscinae	strain=4Y14	GCA_015223195.1	2866724	2866724	type	True	76.3912	79	1423	95	below_threshold
Chromobacterium vaccinii	strain=MWU205	GCA_000971335.1	1108595	1108595	type	True	76.3835	101	1423	95	below_threshold
Chitinimonas taiwanensis	strain=DSM 18899	GCA_900119825.1	240412	240412	type	True	76.3255	117	1423	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	76.2949	130	1423	95	below_threshold
Silvimonas terrae	strain=DSM 18233	GCA_014202765.1	300266	300266	type	True	76.2441	72	1423	95	below_threshold
Chitinilyticum litopenaei	strain=DSM 21440	GCA_000428145.1	1121276	1121276	type	True	76.2316	87	1423	95	below_threshold
Aquitalea pelogenes	strain=CCM 7557	GCA_001515305.1	1293573	1293573	type	True	76.1629	106	1423	95	below_threshold
Chitinimonas arctica	strain=R3-44	GCA_007431345.1	2594795	2594795	type	True	76.0993	98	1423	95	below_threshold
Aquitalea aquatilis	strain=THG-DN7.12	GCA_005155025.1	1537400	1537400	type	True	75.9558	115	1423	95	below_threshold
Massilia soli	strain=R798	GCA_016809835.2	2792854	2792854	type	True	75.4582	50	1423	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:19,261] [INFO] DFAST Taxonomy check result was written to GCF_014202905.1_ASM1420290v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:19,261] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:19,261] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:19,261] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf407e9b0-458e-426a-bac8-28e2afacde2d/dqc_reference/checkm_data
[2024-01-24 13:37:19,263] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:19,303] [INFO] Task started: CheckM
[2024-01-24 13:37:19,303] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202905.1_ASM1420290v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202905.1_ASM1420290v1_genomic.fna/checkm_input GCF_014202905.1_ASM1420290v1_genomic.fna/checkm_result
[2024-01-24 13:38:07,120] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:07,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:07,137] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:07,137] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:07,138] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202905.1_ASM1420290v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:07,138] [INFO] Task started: Blastn
[2024-01-24 13:38:07,138] [INFO] Running command: blastn -query GCF_014202905.1_ASM1420290v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf407e9b0-458e-426a-bac8-28e2afacde2d/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202905.1_ASM1420290v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:08,374] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:08,378] [INFO] Selected 23 target genomes.
[2024-01-24 13:38:08,378] [INFO] Target genome list was writen to GCF_014202905.1_ASM1420290v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:08,424] [INFO] Task started: fastANI
[2024-01-24 13:38:08,424] [INFO] Running command: fastANI --query /var/lib/cwl/stgd25eff42-5794-48eb-a0f4-2505e8d6a986/GCF_014202905.1_ASM1420290v1_genomic.fna.gz --refList GCF_014202905.1_ASM1420290v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202905.1_ASM1420290v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:23,501] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:23,511] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:23,511] [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_014202905.1	s__Chitinivorax tropicus	100.0	1418	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SCOH01;g__Chitinivorax	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005503445.1	s__Chitinivorax sp005503445	79.1482	535	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__SCOH01;g__Chitinivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015223195.1	s__Chitinilyticum litopenaei_A	76.3615	79	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119825.1	s__Chitinimonas taiwanensis	76.3255	117	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas	95.0	96.92	96.91	0.93	0.93	3	-
GCF_000428465.1	s__Chitinimonas koreensis	76.2949	130	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176275.1	s__Andreprevotia lacus	76.2454	108	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Andreprevotia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202765.1	s__Silvimonas terrae	76.2441	72	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Silvimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428145.1	s__Chitinilyticum litopenaei	76.2316	87	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinilyticum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007431345.1	s__Chitinimonas arctica	76.0993	98	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__Chitinimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019234745.1	s__JAFAKZ01 sp019234745	75.8925	60	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinimonadaceae;g__JAFAKZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007833355.1	s__Denitratisoma sp007833355	75.524	61	1423	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Denitratisoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:23,513] [INFO] GTDB search result was written to GCF_014202905.1_ASM1420290v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:23,513] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:23,517] [INFO] DFAST_QC result json was written to GCF_014202905.1_ASM1420290v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:23,517] [INFO] DFAST_QC completed!
[2024-01-24 13:38:23,517] [INFO] Total running time: 0h1m40s