[2023-06-27 22:32:03,054] [INFO] DFAST_QC pipeline started.
[2023-06-27 22:32:03,056] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 22:32:03,056] [INFO] DQC Reference Directory: /var/lib/cwl/stg1bbd3bde-697c-44e0-91e3-8274b53ce011/dqc_reference
[2023-06-27 22:32:04,256] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 22:32:04,257] [INFO] Task started: Prodigal
[2023-06-27 22:32:04,257] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1fc73f5-9287-463f-bd3a-f7f6d7107bb9/GCA_026708645.1_ASM2670864v1_genomic.fna.gz | prodigal -d GCA_026708645.1_ASM2670864v1_genomic.fna/cds.fna -a GCA_026708645.1_ASM2670864v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 22:32:11,815] [INFO] Task succeeded: Prodigal
[2023-06-27 22:32:11,815] [INFO] Task started: HMMsearch
[2023-06-27 22:32:11,816] [INFO] Running command: hmmsearch --tblout GCA_026708645.1_ASM2670864v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1bbd3bde-697c-44e0-91e3-8274b53ce011/dqc_reference/reference_markers.hmm GCA_026708645.1_ASM2670864v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 22:32:12,084] [INFO] Task succeeded: HMMsearch
[2023-06-27 22:32:12,086] [INFO] Found 6/6 markers.
[2023-06-27 22:32:12,113] [INFO] Query marker FASTA was written to GCA_026708645.1_ASM2670864v1_genomic.fna/markers.fasta
[2023-06-27 22:32:12,114] [INFO] Task started: Blastn
[2023-06-27 22:32:12,114] [INFO] Running command: blastn -query GCA_026708645.1_ASM2670864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bbd3bde-697c-44e0-91e3-8274b53ce011/dqc_reference/reference_markers.fasta -out GCA_026708645.1_ASM2670864v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:32:12,823] [INFO] Task succeeded: Blastn
[2023-06-27 22:32:12,828] [INFO] Selected 30 target genomes.
[2023-06-27 22:32:12,829] [INFO] Target genome list was writen to GCA_026708645.1_ASM2670864v1_genomic.fna/target_genomes.txt
[2023-06-27 22:32:12,844] [INFO] Task started: fastANI
[2023-06-27 22:32:12,844] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1fc73f5-9287-463f-bd3a-f7f6d7107bb9/GCA_026708645.1_ASM2670864v1_genomic.fna.gz --refList GCA_026708645.1_ASM2670864v1_genomic.fna/target_genomes.txt --output GCA_026708645.1_ASM2670864v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 22:32:35,832] [INFO] Task succeeded: fastANI
[2023-06-27 22:32:35,833] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1bbd3bde-697c-44e0-91e3-8274b53ce011/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 22:32:35,833] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1bbd3bde-697c-44e0-91e3-8274b53ce011/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 22:32:35,848] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 22:32:35,848] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 22:32:35,848] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	77.0263	111	849	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.3647	82	849	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.1832	76	849	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.1252	97	849	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.1071	113	849	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.8482	79	849	95	below_threshold
Glycomyces xiaoerkulensis	strain=TRM 41368	GCA_002798405.1	2038139	2038139	type	True	75.5546	71	849	95	below_threshold
Actinocatenispora sera	strain=NBRC 101916	GCA_018324685.1	390989	390989	type	True	75.3475	83	849	95	below_threshold
Allokutzneria albata	strain=DSM 44149	GCA_900103775.1	211114	211114	type	True	75.3183	72	849	95	below_threshold
Actinoalloteichus hoggarensis	strain=DSM 45943	GCA_002234535.1	1470176	1470176	type	True	75.2756	53	849	95	below_threshold
Actinocatenispora sera	strain=NRRL B-24477	GCA_000720965.1	390989	390989	type	True	75.2542	82	849	95	below_threshold
Ramlibacter monticola	strain=KACC 19175	GCA_016722785.1	1926872	1926872	type	True	75.246	58	849	95	below_threshold
Nonomuraea antri	strain=NN258	GCA_013283785.1	2730852	2730852	type	True	75.2359	99	849	95	below_threshold
Allokutzneria albata	strain=NRRL B-24461	GCA_000720955.1	211114	211114	type	True	75.1685	68	849	95	below_threshold
Actinoalloteichus hoggarensis	strain=CECT 8639	GCA_014203625.1	1470176	1470176	type	True	75.1226	51	849	95	below_threshold
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	75.079	100	849	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	75.0032	60	849	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 22:32:35,859] [INFO] DFAST Taxonomy check result was written to GCA_026708645.1_ASM2670864v1_genomic.fna/tc_result.tsv
[2023-06-27 22:32:35,859] [INFO] ===== Taxonomy check completed =====
[2023-06-27 22:32:35,860] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 22:32:35,860] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1bbd3bde-697c-44e0-91e3-8274b53ce011/dqc_reference/checkm_data
[2023-06-27 22:32:35,861] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 22:32:35,895] [INFO] Task started: CheckM
[2023-06-27 22:32:35,895] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026708645.1_ASM2670864v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026708645.1_ASM2670864v1_genomic.fna/checkm_input GCA_026708645.1_ASM2670864v1_genomic.fna/checkm_result
[2023-06-27 22:33:05,148] [INFO] Task succeeded: CheckM
[2023-06-27 22:33:05,149] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 22:33:05,170] [INFO] ===== Completeness check finished =====
[2023-06-27 22:33:05,171] [INFO] ===== Start GTDB Search =====
[2023-06-27 22:33:05,171] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026708645.1_ASM2670864v1_genomic.fna/markers.fasta)
[2023-06-27 22:33:05,171] [INFO] Task started: Blastn
[2023-06-27 22:33:05,172] [INFO] Running command: blastn -query GCA_026708645.1_ASM2670864v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1bbd3bde-697c-44e0-91e3-8274b53ce011/dqc_reference/reference_markers_gtdb.fasta -out GCA_026708645.1_ASM2670864v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 22:33:06,205] [INFO] Task succeeded: Blastn
[2023-06-27 22:33:06,209] [INFO] Selected 13 target genomes.
[2023-06-27 22:33:06,210] [INFO] Target genome list was writen to GCA_026708645.1_ASM2670864v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 22:33:06,220] [INFO] Task started: fastANI
[2023-06-27 22:33:06,220] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1fc73f5-9287-463f-bd3a-f7f6d7107bb9/GCA_026708645.1_ASM2670864v1_genomic.fna.gz --refList GCA_026708645.1_ASM2670864v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026708645.1_ASM2670864v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 22:33:14,040] [INFO] Task succeeded: fastANI
[2023-06-27 22:33:14,062] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 22:33:14,063] [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_009844405.1	s__VYCW01 sp009844405	79.5339	430	849	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	99.44	99.17	0.93	0.90	7	-
GCA_009842325.1	s__VYCW01 sp009842325	79.3624	407	849	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	99.89	99.81	0.98	0.97	3	-
GCA_009843915.1	s__VYCW01 sp009843915	79.3395	346	849	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	97.45	96.57	0.82	0.78	5	-
GCA_009837445.1	s__VYCW01 sp009837445	79.1947	391	849	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	99.43	98.40	0.97	0.95	9	-
GCA_009835735.1	s__VYCW01 sp009835735	79.1369	337	849	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	99.69	99.63	0.88	0.85	3	-
GCA_009843735.1	s__VYCW01 sp009843735	79.0667	340	849	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	99.31	99.30	0.93	0.93	3	-
GCA_009840695.1	s__VYCW01 sp009840695	78.1587	143	849	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__VYCW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003697065.1	s__J010 sp003697065	76.9952	116	849	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__J010	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902805665.1	s__CADCTB01 sp902805665	76.2401	62	849	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__AC-14;g__CADCTB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016700055.1	s__Kalu-18 sp016700055	76.0574	86	849	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Kalu-18	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862275.1	s__Actinoplanes nipponensis	75.0616	104	849	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 22:33:14,065] [INFO] GTDB search result was written to GCA_026708645.1_ASM2670864v1_genomic.fna/result_gtdb.tsv
[2023-06-27 22:33:14,066] [INFO] ===== GTDB Search completed =====
[2023-06-27 22:33:14,073] [INFO] DFAST_QC result json was written to GCA_026708645.1_ASM2670864v1_genomic.fna/dqc_result.json
[2023-06-27 22:33:14,074] [INFO] DFAST_QC completed!
[2023-06-27 22:33:14,074] [INFO] Total running time: 0h1m11s