[2024-01-24 10:47:40,955] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:40,957] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:40,957] [INFO] DQC Reference Directory: /var/lib/cwl/stg61f8fc84-e2d1-4fa5-8963-9483c9baa29a/dqc_reference
[2024-01-24 10:47:44,786] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:44,789] [INFO] Task started: Prodigal
[2024-01-24 10:47:44,789] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe91b0ca-9712-45b2-9662-ecf73b91c45d/GCF_015330165.1_ASM1533016v1_genomic.fna.gz | prodigal -d GCF_015330165.1_ASM1533016v1_genomic.fna/cds.fna -a GCF_015330165.1_ASM1533016v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:48:03,904] [INFO] Task succeeded: Prodigal
[2024-01-24 10:48:03,904] [INFO] Task started: HMMsearch
[2024-01-24 10:48:03,904] [INFO] Running command: hmmsearch --tblout GCF_015330165.1_ASM1533016v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61f8fc84-e2d1-4fa5-8963-9483c9baa29a/dqc_reference/reference_markers.hmm GCF_015330165.1_ASM1533016v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:48:04,208] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:48:04,209] [INFO] Found 6/6 markers.
[2024-01-24 10:48:04,253] [INFO] Query marker FASTA was written to GCF_015330165.1_ASM1533016v1_genomic.fna/markers.fasta
[2024-01-24 10:48:04,254] [INFO] Task started: Blastn
[2024-01-24 10:48:04,254] [INFO] Running command: blastn -query GCF_015330165.1_ASM1533016v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61f8fc84-e2d1-4fa5-8963-9483c9baa29a/dqc_reference/reference_markers.fasta -out GCF_015330165.1_ASM1533016v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:04,916] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:04,920] [INFO] Selected 12 target genomes.
[2024-01-24 10:48:04,920] [INFO] Target genome list was writen to GCF_015330165.1_ASM1533016v1_genomic.fna/target_genomes.txt
[2024-01-24 10:48:04,924] [INFO] Task started: fastANI
[2024-01-24 10:48:04,924] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe91b0ca-9712-45b2-9662-ecf73b91c45d/GCF_015330165.1_ASM1533016v1_genomic.fna.gz --refList GCF_015330165.1_ASM1533016v1_genomic.fna/target_genomes.txt --output GCF_015330165.1_ASM1533016v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:15,745] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:15,746] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61f8fc84-e2d1-4fa5-8963-9483c9baa29a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:15,746] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61f8fc84-e2d1-4fa5-8963-9483c9baa29a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:15,756] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:48:15,757] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:48:15,757] [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
Zobellia roscoffensis	strain=Asnod1-F08	GCA_015330165.1	2779508	2779508	type	True	100.0	1659	1659	95	conclusive
Zobellia nedashkovskayae	strain=Asnod2-B07-B	GCA_015330125.1	2779510	2779510	type	True	82.9961	1072	1659	95	below_threshold
Zobellia amurskyensis	strain=KMM 3526	GCA_009725985.1	248905	248905	type	True	82.8102	1100	1659	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	82.1189	1073	1659	95	below_threshold
Zobellia russellii	strain=KMM 3677	GCA_018728565.1	248907	248907	type	True	82.0954	1066	1659	95	below_threshold
Zobellia laminariae	strain=KMM 3676	GCA_009725995.1	248906	248906	type	True	82.0939	1120	1659	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	76.5431	69	1659	95	below_threshold
Muricauda onchidii	strain=XY-359	GCA_004804315.1	2562684	2562684	type	True	76.4518	97	1659	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	76.4411	60	1659	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.1582	57	1659	95	below_threshold
Aquimarina pacifica	strain=SW150	GCA_000520955.1	1296415	1296415	type	True	76.0393	66	1659	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:15,758] [INFO] DFAST Taxonomy check result was written to GCF_015330165.1_ASM1533016v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:15,759] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:15,759] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:15,759] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61f8fc84-e2d1-4fa5-8963-9483c9baa29a/dqc_reference/checkm_data
[2024-01-24 10:48:15,760] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:15,806] [INFO] Task started: CheckM
[2024-01-24 10:48:15,806] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015330165.1_ASM1533016v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015330165.1_ASM1533016v1_genomic.fna/checkm_input GCF_015330165.1_ASM1533016v1_genomic.fna/checkm_result
[2024-01-24 10:49:10,685] [INFO] Task succeeded: CheckM
[2024-01-24 10:49:10,686] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:49:10,708] [INFO] ===== Completeness check finished =====
[2024-01-24 10:49:10,709] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:49:10,709] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015330165.1_ASM1533016v1_genomic.fna/markers.fasta)
[2024-01-24 10:49:10,710] [INFO] Task started: Blastn
[2024-01-24 10:49:10,710] [INFO] Running command: blastn -query GCF_015330165.1_ASM1533016v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61f8fc84-e2d1-4fa5-8963-9483c9baa29a/dqc_reference/reference_markers_gtdb.fasta -out GCF_015330165.1_ASM1533016v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:11,595] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:11,600] [INFO] Selected 10 target genomes.
[2024-01-24 10:49:11,600] [INFO] Target genome list was writen to GCF_015330165.1_ASM1533016v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:49:11,609] [INFO] Task started: fastANI
[2024-01-24 10:49:11,609] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe91b0ca-9712-45b2-9662-ecf73b91c45d/GCF_015330165.1_ASM1533016v1_genomic.fna.gz --refList GCF_015330165.1_ASM1533016v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015330165.1_ASM1533016v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:49:22,386] [INFO] Task succeeded: fastANI
[2024-01-24 10:49:22,402] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:49:22,403] [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_015330165.1	s__Zobellia sp015330165	100.0	1659	1659	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.41	98.41	0.92	0.92	2	conclusive
GCF_018860745.1	s__Zobellia uliginosa_B	84.9795	1123	1659	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015330125.1	s__Zobellia sp015330125	82.9881	1073	1659	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.14	98.14	0.92	0.92	2	-
GCF_009725985.1	s__Zobellia amurskyensis	82.8099	1100	1659	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	98.14	98.14	0.91	0.91	2	-
GCF_018603515.1	s__Zobellia sp018603515	82.1188	1073	1659	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009725995.1	s__Zobellia laminariae	82.0987	1119	1659	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018728565.1	s__Zobellia russellii	82.0882	1067	1659	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	97.51	97.51	0.91	0.91	2	-
GCF_000520955.1	s__Aquimarina pacifica	76.0393	66	1659	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquimarina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:49:22,405] [INFO] GTDB search result was written to GCF_015330165.1_ASM1533016v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:49:22,406] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:49:22,411] [INFO] DFAST_QC result json was written to GCF_015330165.1_ASM1533016v1_genomic.fna/dqc_result.json
[2024-01-24 10:49:22,412] [INFO] DFAST_QC completed!
[2024-01-24 10:49:22,412] [INFO] Total running time: 0h1m41s