[2024-01-24 11:51:10,123] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:10,125] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:10,126] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5bddde5-f74c-4936-9eea-6fa728c1417c/dqc_reference
[2024-01-24 11:51:11,470] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:11,471] [INFO] Task started: Prodigal
[2024-01-24 11:51:11,471] [INFO] Running command: gunzip -c /var/lib/cwl/stgeecce1bb-d273-483e-9c21-7a7597bf66df/GCF_017254835.1_ASM1725483v1_genomic.fna.gz | prodigal -d GCF_017254835.1_ASM1725483v1_genomic.fna/cds.fna -a GCF_017254835.1_ASM1725483v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:41,128] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:41,129] [INFO] Task started: HMMsearch
[2024-01-24 11:51:41,129] [INFO] Running command: hmmsearch --tblout GCF_017254835.1_ASM1725483v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5bddde5-f74c-4936-9eea-6fa728c1417c/dqc_reference/reference_markers.hmm GCF_017254835.1_ASM1725483v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:41,396] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:41,397] [INFO] Found 6/6 markers.
[2024-01-24 11:51:41,442] [INFO] Query marker FASTA was written to GCF_017254835.1_ASM1725483v1_genomic.fna/markers.fasta
[2024-01-24 11:51:41,443] [INFO] Task started: Blastn
[2024-01-24 11:51:41,443] [INFO] Running command: blastn -query GCF_017254835.1_ASM1725483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5bddde5-f74c-4936-9eea-6fa728c1417c/dqc_reference/reference_markers.fasta -out GCF_017254835.1_ASM1725483v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:42,048] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:42,052] [INFO] Selected 15 target genomes.
[2024-01-24 11:51:42,053] [INFO] Target genome list was writen to GCF_017254835.1_ASM1725483v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:42,073] [INFO] Task started: fastANI
[2024-01-24 11:51:42,074] [INFO] Running command: fastANI --query /var/lib/cwl/stgeecce1bb-d273-483e-9c21-7a7597bf66df/GCF_017254835.1_ASM1725483v1_genomic.fna.gz --refList GCF_017254835.1_ASM1725483v1_genomic.fna/target_genomes.txt --output GCF_017254835.1_ASM1725483v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:55,412] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:55,412] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5bddde5-f74c-4936-9eea-6fa728c1417c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:55,412] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5bddde5-f74c-4936-9eea-6fa728c1417c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:55,422] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:55,423] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:55,423] [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
Algoriphagus aestuariicola	strain=JCM 31546	GCA_017254835.1	1852016	1852016	type	True	100.0	1753	1754	95	conclusive
Algoriphagus oliviformis	strain=H41	GCA_017254915.1	2811231	2811231	type	True	81.1313	1035	1754	95	below_threshold
Algoriphagus terrigena	strain=DSM 22685	GCA_000429445.1	344884	344884	type	True	79.2189	760	1754	95	below_threshold
Algoriphagus lacus	strain=N3	GCA_003583985.1	2056311	2056311	type	True	78.2044	414	1754	95	below_threshold
Algoriphagus litoralis	strain=DSL-12	GCA_003259255.1	2202829	2202829	type	True	77.9564	361	1754	95	below_threshold
Algoriphagus boritolerans	strain=DSM 17298	GCA_900108085.1	308111	308111	type	True	77.9469	346	1754	95	below_threshold
Algoriphagus aquaeductus	strain=T4	GCA_003253485.1	475299	475299	type	True	77.8578	356	1754	95	below_threshold
Algoriphagus alkaliphilus	strain=DSM 22703	GCA_900103735.1	279824	279824	type	True	77.8263	373	1754	95	below_threshold
Algoriphagus iocasae	strain=DSM 102044	GCA_014206875.1	1836499	1836499	type	True	77.7892	172	1754	95	below_threshold
Algoriphagus zhangzhouensis	strain=CGMCC 1.11027	GCA_004366575.1	1073327	1073327	type	True	77.5734	166	1754	95	below_threshold
Algoriphagus zhangzhouensis	strain=DSM 25035	GCA_900148515.1	1073327	1073327	type	True	77.5123	168	1754	95	below_threshold
Algoriphagus vanfongensis	strain=DSM 17529	GCA_000429465.1	426371	426371	type	True	77.4017	201	1754	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:55,425] [INFO] DFAST Taxonomy check result was written to GCF_017254835.1_ASM1725483v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:55,425] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:55,425] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:55,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5bddde5-f74c-4936-9eea-6fa728c1417c/dqc_reference/checkm_data
[2024-01-24 11:51:55,426] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:55,474] [INFO] Task started: CheckM
[2024-01-24 11:51:55,474] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017254835.1_ASM1725483v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017254835.1_ASM1725483v1_genomic.fna/checkm_input GCF_017254835.1_ASM1725483v1_genomic.fna/checkm_result
[2024-01-24 11:53:12,354] [INFO] Task succeeded: CheckM
[2024-01-24 11:53:12,355] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:53:12,374] [INFO] ===== Completeness check finished =====
[2024-01-24 11:53:12,374] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:53:12,375] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017254835.1_ASM1725483v1_genomic.fna/markers.fasta)
[2024-01-24 11:53:12,375] [INFO] Task started: Blastn
[2024-01-24 11:53:12,375] [INFO] Running command: blastn -query GCF_017254835.1_ASM1725483v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5bddde5-f74c-4936-9eea-6fa728c1417c/dqc_reference/reference_markers_gtdb.fasta -out GCF_017254835.1_ASM1725483v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:53:13,125] [INFO] Task succeeded: Blastn
[2024-01-24 11:53:13,128] [INFO] Selected 13 target genomes.
[2024-01-24 11:53:13,128] [INFO] Target genome list was writen to GCF_017254835.1_ASM1725483v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:53:13,136] [INFO] Task started: fastANI
[2024-01-24 11:53:13,136] [INFO] Running command: fastANI --query /var/lib/cwl/stgeecce1bb-d273-483e-9c21-7a7597bf66df/GCF_017254835.1_ASM1725483v1_genomic.fna.gz --refList GCF_017254835.1_ASM1725483v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017254835.1_ASM1725483v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:24,961] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:24,972] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:24,973] [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_017254835.1	s__Algoriphagus aestuariicola	100.0	1753	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017254915.1	s__Algoriphagus sp017254915	81.1377	1034	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429445.1	s__Algoriphagus terrigena	79.2367	757	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002735.1	s__Algoriphagus sp002002735	79.108	610	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583985.1	s__Algoriphagus lacus	78.2032	413	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259255.1	s__Algoriphagus litoralis	77.9564	361	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108085.1	s__Algoriphagus boritolerans	77.9469	346	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.80	99.80	0.99	0.99	2	-
GCF_003253485.1	s__Algoriphagus aquaeductus	77.8578	356	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103735.1	s__Algoriphagus alkaliphilus	77.8237	374	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.41	99.41	0.93	0.93	2	-
GCF_014206875.1	s__Algoriphagus iocasae	77.7681	174	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018336015.1	s__Algoriphagus sp018336015	77.6503	316	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900148515.1	s__Algoriphagus zhangzhouensis	77.5088	169	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000381545.1	s__Rhodonellum psychrophilum	76.2915	76	1754	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Rhodonellum	95.0	99.99	99.99	1.00	0.99	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:24,974] [INFO] GTDB search result was written to GCF_017254835.1_ASM1725483v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:24,975] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:24,978] [INFO] DFAST_QC result json was written to GCF_017254835.1_ASM1725483v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:24,979] [INFO] DFAST_QC completed!
[2024-01-24 11:53:24,979] [INFO] Total running time: 0h2m15s