[2024-01-24 12:27:18,697] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:27:18,699] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:27:18,699] [INFO] DQC Reference Directory: /var/lib/cwl/stg260abc95-d1f8-42e9-b5cb-ffd8cb685bb3/dqc_reference
[2024-01-24 12:27:19,871] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:27:19,872] [INFO] Task started: Prodigal
[2024-01-24 12:27:19,872] [INFO] Running command: gunzip -c /var/lib/cwl/stg70a7014f-147c-442c-871b-2e5cc61c55f1/GCF_007747795.1_ASM774779v1_genomic.fna.gz | prodigal -d GCF_007747795.1_ASM774779v1_genomic.fna/cds.fna -a GCF_007747795.1_ASM774779v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:27:42,161] [INFO] Task succeeded: Prodigal
[2024-01-24 12:27:42,162] [INFO] Task started: HMMsearch
[2024-01-24 12:27:42,162] [INFO] Running command: hmmsearch --tblout GCF_007747795.1_ASM774779v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg260abc95-d1f8-42e9-b5cb-ffd8cb685bb3/dqc_reference/reference_markers.hmm GCF_007747795.1_ASM774779v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:27:42,454] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:27:42,457] [INFO] Found 6/6 markers.
[2024-01-24 12:27:42,511] [INFO] Query marker FASTA was written to GCF_007747795.1_ASM774779v1_genomic.fna/markers.fasta
[2024-01-24 12:27:42,512] [INFO] Task started: Blastn
[2024-01-24 12:27:42,512] [INFO] Running command: blastn -query GCF_007747795.1_ASM774779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg260abc95-d1f8-42e9-b5cb-ffd8cb685bb3/dqc_reference/reference_markers.fasta -out GCF_007747795.1_ASM774779v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:27:43,090] [INFO] Task succeeded: Blastn
[2024-01-24 12:27:43,094] [INFO] Selected 24 target genomes.
[2024-01-24 12:27:43,095] [INFO] Target genome list was writen to GCF_007747795.1_ASM774779v1_genomic.fna/target_genomes.txt
[2024-01-24 12:27:43,132] [INFO] Task started: fastANI
[2024-01-24 12:27:43,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg70a7014f-147c-442c-871b-2e5cc61c55f1/GCF_007747795.1_ASM774779v1_genomic.fna.gz --refList GCF_007747795.1_ASM774779v1_genomic.fna/target_genomes.txt --output GCF_007747795.1_ASM774779v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:28:05,798] [INFO] Task succeeded: fastANI
[2024-01-24 12:28:05,799] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg260abc95-d1f8-42e9-b5cb-ffd8cb685bb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:28:05,799] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg260abc95-d1f8-42e9-b5cb-ffd8cb685bb3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:28:05,811] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:28:05,812] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:28:05,812] [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
Maioricimonas rarisocia	strain=Mal4	GCA_007747795.1	2528026	2528026	type	True	100.0	2581	2581	95	conclusive
Rubinisphaera brasiliensis	strain=DSM 5305	GCA_000165715.3	119	119	type	True	76.4031	128	2581	95	below_threshold
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	76.383	234	2581	95	below_threshold
Planctomicrobium piriforme	strain=DSM 26348	GCA_900113665.1	1576369	1576369	type	True	76.3761	194	2581	95	below_threshold
Rubinisphaera margarita	strain=ICM_H10	GCA_022267515.1	2909586	2909586	type	True	76.266	173	2581	95	below_threshold
Alienimonas chondri	strain=LzC2	GCA_013036045.1	2681879	2681879	type	True	76.1098	134	2581	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	76.0376	111	2581	95	below_threshold
Thalassoglobus neptunius	strain=KOR42	GCA_007859735.1	1938619	1938619	type	True	75.9822	82	2581	95	below_threshold
Calycomorphotria hydatis	strain=V22	GCA_007745435.1	2528027	2528027	type	True	75.9706	98	2581	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	75.8895	91	2581	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.7204	153	2581	95	below_threshold
Fuerstiella marisgermanici	strain=NH11	GCA_001983935.1	1891926	1891926	type	True	75.5773	84	2581	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	74.8989	58	2581	95	below_threshold
Nocardia harenae	strain=NBRC 108248	GCA_001612885.1	358707	358707	type	True	74.8094	60	2581	95	below_threshold
Arenimonas composti	strain=DSM 18010	GCA_000426365.1	370776	370776	type	True	74.7469	59	2581	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:28:05,813] [INFO] DFAST Taxonomy check result was written to GCF_007747795.1_ASM774779v1_genomic.fna/tc_result.tsv
[2024-01-24 12:28:05,814] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:28:05,814] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:28:05,814] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg260abc95-d1f8-42e9-b5cb-ffd8cb685bb3/dqc_reference/checkm_data
[2024-01-24 12:28:05,815] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:28:05,883] [INFO] Task started: CheckM
[2024-01-24 12:28:05,884] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007747795.1_ASM774779v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007747795.1_ASM774779v1_genomic.fna/checkm_input GCF_007747795.1_ASM774779v1_genomic.fna/checkm_result
[2024-01-24 12:29:27,585] [INFO] Task succeeded: CheckM
[2024-01-24 12:29:27,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:29:27,607] [INFO] ===== Completeness check finished =====
[2024-01-24 12:29:27,608] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:29:27,608] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007747795.1_ASM774779v1_genomic.fna/markers.fasta)
[2024-01-24 12:29:27,608] [INFO] Task started: Blastn
[2024-01-24 12:29:27,608] [INFO] Running command: blastn -query GCF_007747795.1_ASM774779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg260abc95-d1f8-42e9-b5cb-ffd8cb685bb3/dqc_reference/reference_markers_gtdb.fasta -out GCF_007747795.1_ASM774779v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:28,446] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:28,450] [INFO] Selected 24 target genomes.
[2024-01-24 12:29:28,450] [INFO] Target genome list was writen to GCF_007747795.1_ASM774779v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:29:28,542] [INFO] Task started: fastANI
[2024-01-24 12:29:28,542] [INFO] Running command: fastANI --query /var/lib/cwl/stg70a7014f-147c-442c-871b-2e5cc61c55f1/GCF_007747795.1_ASM774779v1_genomic.fna.gz --refList GCF_007747795.1_ASM774779v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007747795.1_ASM774779v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:29:55,257] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:55,271] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:29:55,271] [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_007747795.1	s__Maioricimonas rarisocia	100.0	2581	2581	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Maioricimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003388505.1	s__MB-PLM-1 sp003388505	76.4593	321	2581	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__MB-PLM-1	95.0	99.82	99.66	0.97	0.95	4	-
GCF_001610835.1	s__Planctomyces_A sp001610835	76.3911	329	2581	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctomyces_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113665.1	s__Planctomicrobium piriforme	76.3787	195	2581	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Planctomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007745175.1	s__Caulifigura coniformis	76.3649	235	2581	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Caulifigura	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795125.1	s__JAEUIG01 sp016795125	76.2829	214	2581	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JAEUIG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003671275.1	s__TH-plancto1 sp003671275	76.1885	124	2581	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__TH-plancto1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013813775.1	s__JACCRE01 sp013813775	75.7602	174	2581	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__JACCRE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003445035.1	s__UBA8437 sp003445035	75.7586	128	2581	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001983935.1	s__Fuerstia marisgermanicae	75.4619	83	2581	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Fuerstia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005798445.1	s__SXKJ01 sp005798445	75.4237	121	2581	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXKJ01	95.0	99.80	99.80	0.90	0.90	2	-
GCA_002724415.1	s__UBA8437 sp002724415	75.387	96	2581	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__UBA8437	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005778405.1	s__SXOA01 sp005778405	75.3211	60	2581	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__SXOA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005778225.1	s__SXPC01 sp005778225	75.1399	62	2581	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXPC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019237095.1	s__JAFAHT01 sp019237095	75.01	60	2581	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__JAFAHT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002305855.1	s__Melittangium boletus	74.8052	67	2581	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Myxococcaceae;g__Melittangium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:29:55,274] [INFO] GTDB search result was written to GCF_007747795.1_ASM774779v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:29:55,275] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:29:55,279] [INFO] DFAST_QC result json was written to GCF_007747795.1_ASM774779v1_genomic.fna/dqc_result.json
[2024-01-24 12:29:55,279] [INFO] DFAST_QC completed!
[2024-01-24 12:29:55,279] [INFO] Total running time: 0h2m37s