[2023-06-28 20:26:40,115] [INFO] DFAST_QC pipeline started.
[2023-06-28 20:26:40,121] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 20:26:40,121] [INFO] DQC Reference Directory: /var/lib/cwl/stgafd06924-26f7-42b9-8e7b-7d905c98ad4b/dqc_reference
[2023-06-28 20:26:41,363] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 20:26:41,364] [INFO] Task started: Prodigal
[2023-06-28 20:26:41,364] [INFO] Running command: gunzip -c /var/lib/cwl/stg22652709-eac9-418e-827a-3c59fc7a660e/GCA_002708585.1_ASM270858v1_genomic.fna.gz | prodigal -d GCA_002708585.1_ASM270858v1_genomic.fna/cds.fna -a GCA_002708585.1_ASM270858v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 20:26:50,950] [INFO] Task succeeded: Prodigal
[2023-06-28 20:26:50,950] [INFO] Task started: HMMsearch
[2023-06-28 20:26:50,950] [INFO] Running command: hmmsearch --tblout GCA_002708585.1_ASM270858v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgafd06924-26f7-42b9-8e7b-7d905c98ad4b/dqc_reference/reference_markers.hmm GCA_002708585.1_ASM270858v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 20:26:51,202] [INFO] Task succeeded: HMMsearch
[2023-06-28 20:26:51,203] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg22652709-eac9-418e-827a-3c59fc7a660e/GCA_002708585.1_ASM270858v1_genomic.fna.gz]
[2023-06-28 20:26:51,243] [INFO] Query marker FASTA was written to GCA_002708585.1_ASM270858v1_genomic.fna/markers.fasta
[2023-06-28 20:26:51,243] [INFO] Task started: Blastn
[2023-06-28 20:26:51,243] [INFO] Running command: blastn -query GCA_002708585.1_ASM270858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafd06924-26f7-42b9-8e7b-7d905c98ad4b/dqc_reference/reference_markers.fasta -out GCA_002708585.1_ASM270858v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:26:51,898] [INFO] Task succeeded: Blastn
[2023-06-28 20:26:51,903] [INFO] Selected 14 target genomes.
[2023-06-28 20:26:51,903] [INFO] Target genome list was writen to GCA_002708585.1_ASM270858v1_genomic.fna/target_genomes.txt
[2023-06-28 20:26:51,912] [INFO] Task started: fastANI
[2023-06-28 20:26:51,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg22652709-eac9-418e-827a-3c59fc7a660e/GCA_002708585.1_ASM270858v1_genomic.fna.gz --refList GCA_002708585.1_ASM270858v1_genomic.fna/target_genomes.txt --output GCA_002708585.1_ASM270858v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 20:27:04,306] [INFO] Task succeeded: fastANI
[2023-06-28 20:27:04,307] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgafd06924-26f7-42b9-8e7b-7d905c98ad4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 20:27:04,307] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgafd06924-26f7-42b9-8e7b-7d905c98ad4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 20:27:04,320] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 20:27:04,320] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 20:27:04,320] [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
Hyphomonas atlantica	strain=22II1-22F38	GCA_000682715.1	1280948	1280948	type	True	82.447	641	1046	95	below_threshold
Hyphomonas beringensis	strain=25B14_1	GCA_000682755.1	1280946	1280946	type	True	80.1699	530	1046	95	below_threshold
Hyphomonas pacifica	strain=T16B2	GCA_000682675.1	1280941	1280941	type	True	79.6497	506	1046	95	below_threshold
Hyphomonas jannaschiana	strain=VP2	GCA_000685215.1	86	86	type	True	78.9171	425	1046	95	below_threshold
Hyphomonas adhaerens	strain=MHS-3	GCA_000685235.1	81029	81029	type	True	78.8195	404	1046	95	below_threshold
Hyphomonas chukchiensis	strain=BH-BN04-4	GCA_000682695.1	1280947	1280947	type	True	78.6041	404	1046	95	below_threshold
Hyphomonas johnsonii	strain=MHS-2	GCA_000685275.1	81031	81031	type	True	78.453	374	1046	95	below_threshold
Hyphomonas oceanitis	strain=SCH89	GCA_000685295.1	81033	81033	type	True	78.443	408	1046	95	below_threshold
Henriciella aquimarina	strain=LMG 24711	GCA_002088975.1	545261	545261	type	True	77.7723	238	1046	95	below_threshold
Hyphomonas sediminis	strain=WL0036	GCA_019679475.1	2866160	2866160	type	True	77.4942	274	1046	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	75.9944	55	1046	95	below_threshold
Rhizobium redzepovicii	strain=18T	GCA_019793435.1	2867518	2867518	type	True	75.6751	54	1046	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	75.6625	55	1046	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	75.2341	56	1046	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 20:27:04,323] [INFO] DFAST Taxonomy check result was written to GCA_002708585.1_ASM270858v1_genomic.fna/tc_result.tsv
[2023-06-28 20:27:04,324] [INFO] ===== Taxonomy check completed =====
[2023-06-28 20:27:04,324] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 20:27:04,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgafd06924-26f7-42b9-8e7b-7d905c98ad4b/dqc_reference/checkm_data
[2023-06-28 20:27:04,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 20:27:04,363] [INFO] Task started: CheckM
[2023-06-28 20:27:04,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002708585.1_ASM270858v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002708585.1_ASM270858v1_genomic.fna/checkm_input GCA_002708585.1_ASM270858v1_genomic.fna/checkm_result
[2023-06-28 20:27:36,628] [INFO] Task succeeded: CheckM
[2023-06-28 20:27:36,630] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 20:27:36,655] [INFO] ===== Completeness check finished =====
[2023-06-28 20:27:36,655] [INFO] ===== Start GTDB Search =====
[2023-06-28 20:27:36,655] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002708585.1_ASM270858v1_genomic.fna/markers.fasta)
[2023-06-28 20:27:36,656] [INFO] Task started: Blastn
[2023-06-28 20:27:36,656] [INFO] Running command: blastn -query GCA_002708585.1_ASM270858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgafd06924-26f7-42b9-8e7b-7d905c98ad4b/dqc_reference/reference_markers_gtdb.fasta -out GCA_002708585.1_ASM270858v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 20:27:37,653] [INFO] Task succeeded: Blastn
[2023-06-28 20:27:37,659] [INFO] Selected 10 target genomes.
[2023-06-28 20:27:37,659] [INFO] Target genome list was writen to GCA_002708585.1_ASM270858v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 20:27:37,669] [INFO] Task started: fastANI
[2023-06-28 20:27:37,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg22652709-eac9-418e-827a-3c59fc7a660e/GCA_002708585.1_ASM270858v1_genomic.fna.gz --refList GCA_002708585.1_ASM270858v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002708585.1_ASM270858v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 20:27:45,096] [INFO] Task succeeded: fastANI
[2023-06-28 20:27:45,112] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 20:27:45,112] [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
GCA_002414505.1	s__Hyphomonas sp002414505	98.8198	849	1046	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.04	98.84	0.81	0.74	4	conclusive
GCF_000682775.1	s__Hyphomonas sp000682775	84.7551	737	1046	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	95.72	95.47	0.88	0.83	38	-
GCF_000682715.1	s__Hyphomonas atlantica	82.447	641	1046	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	98.47	98.11	0.91	0.87	6	-
GCA_017792385.1	s__Hyphomonas sp017792385	82.1546	674	1046	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222605.1	s__Hyphomonas sp002695785	80.3289	566	1046	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.58	99.58	0.85	0.85	2	-
GCF_000682755.1	s__Hyphomonas beringensis	80.1666	530	1046	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000682675.1	s__Hyphomonas pacifica	79.6497	506	1046	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.59	99.19	0.95	0.91	3	-
GCA_014763715.1	s__Hyphomonas sp014763715	78.9031	413	1046	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002700305.1	s__Hyphomonas sp002700305	78.8993	415	1046	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.48	99.29	0.92	0.85	3	-
GCF_000682735.1	s__Hyphomonas sp000682735	78.8212	423	1046	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Hyphomonadaceae;g__Hyphomonas	95.0	99.43	99.16	0.91	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-28 20:27:45,114] [INFO] GTDB search result was written to GCA_002708585.1_ASM270858v1_genomic.fna/result_gtdb.tsv
[2023-06-28 20:27:45,115] [INFO] ===== GTDB Search completed =====
[2023-06-28 20:27:45,119] [INFO] DFAST_QC result json was written to GCA_002708585.1_ASM270858v1_genomic.fna/dqc_result.json
[2023-06-28 20:27:45,119] [INFO] DFAST_QC completed!
[2023-06-28 20:27:45,119] [INFO] Total running time: 0h1m5s