[2023-06-27 19:45:31,532] [INFO] DFAST_QC pipeline started.
[2023-06-27 19:45:31,535] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 19:45:31,535] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7b2fd8b-685c-4383-b7a5-0d04c3fe3b43/dqc_reference
[2023-06-27 19:45:32,710] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 19:45:32,711] [INFO] Task started: Prodigal
[2023-06-27 19:45:32,712] [INFO] Running command: gunzip -c /var/lib/cwl/stg9baf3b5a-1d67-41a4-8b2f-8d47c62af611/GCA_026984795.1_ASM2698479v1_genomic.fna.gz | prodigal -d GCA_026984795.1_ASM2698479v1_genomic.fna/cds.fna -a GCA_026984795.1_ASM2698479v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 19:45:46,544] [INFO] Task succeeded: Prodigal
[2023-06-27 19:45:46,545] [INFO] Task started: HMMsearch
[2023-06-27 19:45:46,545] [INFO] Running command: hmmsearch --tblout GCA_026984795.1_ASM2698479v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7b2fd8b-685c-4383-b7a5-0d04c3fe3b43/dqc_reference/reference_markers.hmm GCA_026984795.1_ASM2698479v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 19:45:46,829] [INFO] Task succeeded: HMMsearch
[2023-06-27 19:45:46,831] [INFO] Found 6/6 markers.
[2023-06-27 19:45:46,874] [INFO] Query marker FASTA was written to GCA_026984795.1_ASM2698479v1_genomic.fna/markers.fasta
[2023-06-27 19:45:46,875] [INFO] Task started: Blastn
[2023-06-27 19:45:46,875] [INFO] Running command: blastn -query GCA_026984795.1_ASM2698479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7b2fd8b-685c-4383-b7a5-0d04c3fe3b43/dqc_reference/reference_markers.fasta -out GCA_026984795.1_ASM2698479v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 19:45:47,531] [INFO] Task succeeded: Blastn
[2023-06-27 19:45:47,535] [INFO] Selected 29 target genomes.
[2023-06-27 19:45:47,536] [INFO] Target genome list was writen to GCA_026984795.1_ASM2698479v1_genomic.fna/target_genomes.txt
[2023-06-27 19:45:47,540] [INFO] Task started: fastANI
[2023-06-27 19:45:47,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg9baf3b5a-1d67-41a4-8b2f-8d47c62af611/GCA_026984795.1_ASM2698479v1_genomic.fna.gz --refList GCA_026984795.1_ASM2698479v1_genomic.fna/target_genomes.txt --output GCA_026984795.1_ASM2698479v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 19:46:06,384] [INFO] Task succeeded: fastANI
[2023-06-27 19:46:06,385] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7b2fd8b-685c-4383-b7a5-0d04c3fe3b43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 19:46:06,385] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7b2fd8b-685c-4383-b7a5-0d04c3fe3b43/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 19:46:06,405] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 19:46:06,405] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 19:46:06,406] [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
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	76.3695	68	1705	95	below_threshold
Paludibaculum fermentans	strain=P105	GCA_015277775.1	1473598	1473598	type	True	76.0512	183	1705	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	76.042	54	1705	95	below_threshold
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.4512	102	1705	95	below_threshold
Tepidimonas alkaliphilus	strain=YIM 72238	GCA_007556595.1	2588942	2588942	type	True	75.4319	57	1705	95	below_threshold
Vulgatibacter incomptus	strain=DSM 27710	GCA_001263175.1	1391653	1391653	type	True	75.4218	69	1705	95	below_threshold
Jiella endophytica	strain=CBS5Q-3	GCA_004519335.1	2558362	2558362	type	True	75.3296	71	1705	95	below_threshold
Blastochloris sulfoviridis	strain=DSM 729	GCA_008630065.1	50712	50712	type	True	75.2337	78	1705	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.1967	152	1705	95	below_threshold
Chitinimonas koreensis	strain=DSM 17726	GCA_000428465.1	356302	356302	type	True	75.1573	123	1705	95	below_threshold
Magnetospirillum aberrantis	strain=SpK	GCA_011022235.1	1105283	1105283	type	True	75.1204	59	1705	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_001315015.1	192	192	type	True	75.0958	113	1705	95	below_threshold
Thermaerobacter subterraneus	strain=DSM 13965	GCA_000183545.3	175696	175696	type	True	75.0786	72	1705	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_007827425.1	192	192	type	True	75.0732	117	1705	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_008274945.1	192	192	type	True	75.0713	118	1705	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	75.0612	71	1705	95	below_threshold
Xylophilus ampelinus	strain=CECT 7646	GCA_003217575.1	54067	54067	type	True	75.0525	72	1705	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	75.0353	68	1705	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	75.0042	74	1705	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	74.9781	79	1705	95	below_threshold
Chelatococcus reniformis	strain=CGMCC 1.12919	GCA_014640075.1	1494448	1494448	type	True	74.9589	86	1705	95	below_threshold
Azospirillum brasilense	strain=Sp 7	GCA_002027385.1	192	192	type	True	74.9354	113	1705	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	74.9175	113	1705	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 19:46:06,408] [INFO] DFAST Taxonomy check result was written to GCA_026984795.1_ASM2698479v1_genomic.fna/tc_result.tsv
[2023-06-27 19:46:06,409] [INFO] ===== Taxonomy check completed =====
[2023-06-27 19:46:06,409] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 19:46:06,409] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7b2fd8b-685c-4383-b7a5-0d04c3fe3b43/dqc_reference/checkm_data
[2023-06-27 19:46:06,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 19:46:06,465] [INFO] Task started: CheckM
[2023-06-27 19:46:06,465] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026984795.1_ASM2698479v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026984795.1_ASM2698479v1_genomic.fna/checkm_input GCA_026984795.1_ASM2698479v1_genomic.fna/checkm_result
[2023-06-27 19:46:47,834] [INFO] Task succeeded: CheckM
[2023-06-27 19:46:47,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 19:46:47,865] [INFO] ===== Completeness check finished =====
[2023-06-27 19:46:47,866] [INFO] ===== Start GTDB Search =====
[2023-06-27 19:46:47,866] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026984795.1_ASM2698479v1_genomic.fna/markers.fasta)
[2023-06-27 19:46:47,866] [INFO] Task started: Blastn
[2023-06-27 19:46:47,867] [INFO] Running command: blastn -query GCA_026984795.1_ASM2698479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7b2fd8b-685c-4383-b7a5-0d04c3fe3b43/dqc_reference/reference_markers_gtdb.fasta -out GCA_026984795.1_ASM2698479v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 19:46:48,802] [INFO] Task succeeded: Blastn
[2023-06-27 19:46:48,807] [INFO] Selected 33 target genomes.
[2023-06-27 19:46:48,808] [INFO] Target genome list was writen to GCA_026984795.1_ASM2698479v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 19:46:48,830] [INFO] Task started: fastANI
[2023-06-27 19:46:48,830] [INFO] Running command: fastANI --query /var/lib/cwl/stg9baf3b5a-1d67-41a4-8b2f-8d47c62af611/GCA_026984795.1_ASM2698479v1_genomic.fna.gz --refList GCA_026984795.1_ASM2698479v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026984795.1_ASM2698479v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 19:47:18,141] [INFO] Task succeeded: fastANI
[2023-06-27 19:47:18,169] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 19:47:18,170] [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_016213755.1	s__JACQZT01 sp016213755	76.4229	247	1705	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__JACQZT01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003428625.2	s__Palsa-343 sp003428625	76.3695	68	1705	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-343	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860455.1	s__PNKE01 sp014860455	76.2054	172	1705	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__PNKE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003142185.1	s__Bog-375 sp003142185	76.1072	153	1705	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Bog-375	95.0	99.72	98.50	0.96	0.85	24	-
GCA_003166475.1	s__Bog-159 sp003166475	76.0372	128	1705	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Bog-159	95.0	99.58	99.43	0.89	0.86	9	-
GCA_016871315.1	s__VFZE01 sp016871315	76.0287	170	1705	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__VFZE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268715.1	s__TMP-7 sp018268715	76.0089	233	1705	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__TMP-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000381625.1	s__KBS-96 sp000381625	75.9625	51	1705	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__KBS-96	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002279285.1	s__RBG-13-68-16 sp002279285	75.8584	54	1705	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Thermoanaerobaculales;f__Thermoanaerobaculaceae;g__RBG-13-68-16	95.0	98.89	98.89	0.79	0.79	2	-
GCA_902825945.1	s__SYLY01 sp902825945	75.8403	154	1705	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__SYLY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011054605.1	s__DSOI01 sp011054605	75.7871	203	1705	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__DSOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008682415.1	s__Terracidiphilus sp008682415	75.7801	74	1705	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213775.1	s__CADEFT01 sp016213775	75.7651	116	1705	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__CADEFT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019187195.1	s__CADEFT01 sp019187195	75.7433	140	1705	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__CADEFT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003223115.1	s__QHXW01 sp003223115	75.7015	83	1705	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__QHXW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903925975.1	s__BOG-224 sp903925975	75.6728	108	1705	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__BOG-224	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464575.1	s__Ga0077553 sp001464575	75.5829	98	1705	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Ga0077553	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004298115.1	s__RBG-13-68-16 sp004298115	75.5454	82	1705	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Thermoanaerobaculales;f__Thermoanaerobaculaceae;g__RBG-13-68-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003135055.1	s__PALSA-243 sp003135055	75.393	108	1705	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__PALSA-243	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003133645.1	s__RBG-13-68-16 sp003133645	75.2757	67	1705	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__Thermoanaerobaculales;f__Thermoanaerobaculaceae;g__RBG-13-68-16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019261985.1	s__Palsa-187 sp019261985	75.2621	53	1705	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Palsa-187	95.0	99.77	99.77	0.89	0.89	2	-
GCA_001790205.1	s__GWA2-73-35 sp001790205	75.237	84	1705	d__Bacteria;p__Methylomirabilota;c__Methylomirabilia;o__Rokubacteriales;f__CSP1-6;g__GWA2-73-35	95.0	99.55	99.55	0.88	0.88	2	-
GCA_011367345.1	s__DSYW01 sp011367345	75.1841	58	1705	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Tepidisphaerales;f__Tepidisphaeraceae;g__DSYW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017860005.1	s__JACTMI01 sp017860005	75.1795	98	1705	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__UBA5704;g__JACTMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000183545.2	s__Thermaerobacter subterraneus	75.0993	69	1705	d__Bacteria;p__Firmicutes_E;c__Thermaerobacteria;o__Thermaerobacterales;f__Thermaerobacteraceae;g__Thermaerobacter	95.0	95.08	95.08	0.91	0.91	2	-
GCA_016704465.1	s__SCN-70-22 sp016704465	74.9075	70	1705	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__SCN-70-22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217545.1	s__Actinoplanes cinnamomeus	74.8596	98	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002285795.1	s__KBS50 sp002285795	74.7735	139	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__KBS50	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002065.1	s__Actinoplanes ferrugineus_A	74.6772	148	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	99.31	99.31	0.94	0.94	2	-
GCF_016863475.1	s__Spirilliplanes yamanashiensis	74.6622	150	1705	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Spirilliplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 19:47:18,172] [INFO] GTDB search result was written to GCA_026984795.1_ASM2698479v1_genomic.fna/result_gtdb.tsv
[2023-06-27 19:47:18,172] [INFO] ===== GTDB Search completed =====
[2023-06-27 19:47:18,177] [INFO] DFAST_QC result json was written to GCA_026984795.1_ASM2698479v1_genomic.fna/dqc_result.json
[2023-06-27 19:47:18,178] [INFO] DFAST_QC completed!
[2023-06-27 19:47:18,178] [INFO] Total running time: 0h1m47s