[2023-06-17 10:34:16,185] [INFO] DFAST_QC pipeline started.
[2023-06-17 10:34:16,188] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 10:34:16,188] [INFO] DQC Reference Directory: /var/lib/cwl/stgabca8b6b-3cf4-4b0c-b3fa-c80ee407b480/dqc_reference
[2023-06-17 10:34:17,469] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 10:34:17,470] [INFO] Task started: Prodigal
[2023-06-17 10:34:17,470] [INFO] Running command: gunzip -c /var/lib/cwl/stg60d0d0a9-390e-4392-bae5-f2afc6ff8d68/GCA_013538855.1_ASM1353885v1_genomic.fna.gz | prodigal -d GCA_013538855.1_ASM1353885v1_genomic.fna/cds.fna -a GCA_013538855.1_ASM1353885v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 10:34:37,045] [INFO] Task succeeded: Prodigal
[2023-06-17 10:34:37,045] [INFO] Task started: HMMsearch
[2023-06-17 10:34:37,045] [INFO] Running command: hmmsearch --tblout GCA_013538855.1_ASM1353885v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabca8b6b-3cf4-4b0c-b3fa-c80ee407b480/dqc_reference/reference_markers.hmm GCA_013538855.1_ASM1353885v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 10:34:37,381] [INFO] Task succeeded: HMMsearch
[2023-06-17 10:34:37,382] [INFO] Found 6/6 markers.
[2023-06-17 10:34:37,432] [INFO] Query marker FASTA was written to GCA_013538855.1_ASM1353885v1_genomic.fna/markers.fasta
[2023-06-17 10:34:37,432] [INFO] Task started: Blastn
[2023-06-17 10:34:37,433] [INFO] Running command: blastn -query GCA_013538855.1_ASM1353885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabca8b6b-3cf4-4b0c-b3fa-c80ee407b480/dqc_reference/reference_markers.fasta -out GCA_013538855.1_ASM1353885v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 10:34:38,139] [INFO] Task succeeded: Blastn
[2023-06-17 10:34:38,145] [INFO] Selected 17 target genomes.
[2023-06-17 10:34:38,146] [INFO] Target genome list was writen to GCA_013538855.1_ASM1353885v1_genomic.fna/target_genomes.txt
[2023-06-17 10:34:38,151] [INFO] Task started: fastANI
[2023-06-17 10:34:38,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg60d0d0a9-390e-4392-bae5-f2afc6ff8d68/GCA_013538855.1_ASM1353885v1_genomic.fna.gz --refList GCA_013538855.1_ASM1353885v1_genomic.fna/target_genomes.txt --output GCA_013538855.1_ASM1353885v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 10:34:49,419] [INFO] Task succeeded: fastANI
[2023-06-17 10:34:49,420] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabca8b6b-3cf4-4b0c-b3fa-c80ee407b480/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 10:34:49,421] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabca8b6b-3cf4-4b0c-b3fa-c80ee407b480/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 10:34:49,436] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 10:34:49,437] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 10:34:49,437] [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
Herpetosiphon llansteffanensis	strain=CA052B	GCA_003205875.1	2094568	2094568	type	True	75.7072	78	1968	95	below_threshold
Herpetosiphon geysericola	strain=DSM 7119	GCA_001306135.1	70996	70996	type	True	75.5452	66	1968	95	below_threshold
Herpetosiphon giganteus	strain=DSM 589	GCA_016907925.1	2029754	2029754	type	True	75.4574	76	1968	95	below_threshold
Chloroflexus islandicus	strain=isl-2	GCA_001650695.1	1707952	1707952	type	True	75.3843	85	1968	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	74.8742	59	1968	95	below_threshold
Deinococcus aerolatus	strain=JCM 15442	GCA_014647055.1	522487	522487	type	True	74.7952	66	1968	95	below_threshold
Flexivirga aerilata	strain=ID2601S	GCA_013002715.1	1656889	1656889	type	True	74.7775	56	1968	95	below_threshold
Agromyces hippuratus	strain=DSM 8598	GCA_013410355.1	286438	286438	type	True	74.6574	62	1968	95	below_threshold
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	74.6385	50	1968	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 10:34:49,439] [INFO] DFAST Taxonomy check result was written to GCA_013538855.1_ASM1353885v1_genomic.fna/tc_result.tsv
[2023-06-17 10:34:49,440] [INFO] ===== Taxonomy check completed =====
[2023-06-17 10:34:49,441] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 10:34:49,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabca8b6b-3cf4-4b0c-b3fa-c80ee407b480/dqc_reference/checkm_data
[2023-06-17 10:34:49,443] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 10:34:49,508] [INFO] Task started: CheckM
[2023-06-17 10:34:49,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013538855.1_ASM1353885v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013538855.1_ASM1353885v1_genomic.fna/checkm_input GCA_013538855.1_ASM1353885v1_genomic.fna/checkm_result
[2023-06-17 10:35:46,524] [INFO] Task succeeded: CheckM
[2023-06-17 10:35:46,525] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 10:35:46,550] [INFO] ===== Completeness check finished =====
[2023-06-17 10:35:46,550] [INFO] ===== Start GTDB Search =====
[2023-06-17 10:35:46,551] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013538855.1_ASM1353885v1_genomic.fna/markers.fasta)
[2023-06-17 10:35:46,551] [INFO] Task started: Blastn
[2023-06-17 10:35:46,551] [INFO] Running command: blastn -query GCA_013538855.1_ASM1353885v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabca8b6b-3cf4-4b0c-b3fa-c80ee407b480/dqc_reference/reference_markers_gtdb.fasta -out GCA_013538855.1_ASM1353885v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 10:35:47,352] [INFO] Task succeeded: Blastn
[2023-06-17 10:35:47,357] [INFO] Selected 25 target genomes.
[2023-06-17 10:35:47,357] [INFO] Target genome list was writen to GCA_013538855.1_ASM1353885v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 10:35:47,379] [INFO] Task started: fastANI
[2023-06-17 10:35:47,379] [INFO] Running command: fastANI --query /var/lib/cwl/stg60d0d0a9-390e-4392-bae5-f2afc6ff8d68/GCA_013538855.1_ASM1353885v1_genomic.fna.gz --refList GCA_013538855.1_ASM1353885v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013538855.1_ASM1353885v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 10:36:06,144] [INFO] Task succeeded: fastANI
[2023-06-17 10:36:06,166] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 10:36:06,167] [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_013538855.1	s__OHK22 sp013538855	100.0	1955	1968	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Herpetosiphonaceae;g__OHK22	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013813565.1	s__JACCRK01 sp013813565	77.473	356	1968	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Herpetosiphonaceae;g__JACCRK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717335.1	s__JADKFS01 sp016717335	75.7096	306	1968	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__JADKFS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004138175.2	s__Oscillochloris sp004138175	75.6585	191	1968	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903887465.1	s__Oscillochloris sp903887465	75.5568	127	1968	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	99.82	99.74	0.95	0.93	6	-
GCF_001306135.1	s__Herpetosiphon geysericola	75.5452	66	1968	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Herpetosiphonaceae;g__Herpetosiphon	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001399705.1	s__Kouleothrix aurantiaca	75.4909	72	1968	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__Kouleothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016722075.1	s__Kouleothrix sp016722075	75.4815	255	1968	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__Kouleothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013388805.1	s__JACAEO01 sp013388805	75.4443	140	1968	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__JACAEO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014381165.1	s__JACMIM01 sp014381165	75.3535	78	1968	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__JACMIM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000018565.1	s__Herpetosiphon aurantiacus	75.2276	83	1968	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Herpetosiphonaceae;g__Herpetosiphon	95.0	99.99	99.99	1.00	1.00	2	-
GCA_012031775.1	s__JAAUTF01 sp012031775	75.2151	88	1968	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__JAAUTF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266315.1	s__Kouleothrix sp018266315	75.154	83	1968	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__Kouleothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012031225.1	s__JAAUTZ01 sp012031225	75.0643	57	1968	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__JAAUTZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016781525.1	s__LB3-1 sp016781525	75.0475	53	1968	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Herpetosiphonaceae;g__LB3-1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360575.1	s__JABWBG01 sp013360575	74.8882	56	1968	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__J102;f__J102;g__JABWBG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426385.1	s__Arsenicicoccus bolidensis	74.8742	59	1968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Arsenicicoccus	95.0	98.16	98.06	0.89	0.88	4	-
GCA_002428565.1	s__UBA6092 sp002428565	74.8238	52	1968	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA4823;g__UBA6092	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051445.1	s__DSKJ01 sp011051445	74.7954	53	1968	d__Bacteria;p__Chloroflexota;c__FW602-bin22;o__FW602-bin22;f__DSKJ01;g__DSKJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101335.1	s__Quadrisphaera sp900101335	74.6074	96	1968	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 10:36:06,169] [INFO] GTDB search result was written to GCA_013538855.1_ASM1353885v1_genomic.fna/result_gtdb.tsv
[2023-06-17 10:36:06,170] [INFO] ===== GTDB Search completed =====
[2023-06-17 10:36:06,174] [INFO] DFAST_QC result json was written to GCA_013538855.1_ASM1353885v1_genomic.fna/dqc_result.json
[2023-06-17 10:36:06,174] [INFO] DFAST_QC completed!
[2023-06-17 10:36:06,174] [INFO] Total running time: 0h1m50s