[2023-06-13 07:32:09,996] [INFO] DFAST_QC pipeline started.
[2023-06-13 07:32:09,998] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 07:32:09,998] [INFO] DQC Reference Directory: /var/lib/cwl/stg86c48cdc-adda-4feb-b812-4f369bc36a2f/dqc_reference
[2023-06-13 07:32:11,300] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 07:32:11,301] [INFO] Task started: Prodigal
[2023-06-13 07:32:11,301] [INFO] Running command: gunzip -c /var/lib/cwl/stg9152f558-e8c0-4bcf-a8e9-ce618451b6c5/GCA_022708905.1_ASM2270890v1_genomic.fna.gz | prodigal -d GCA_022708905.1_ASM2270890v1_genomic.fna/cds.fna -a GCA_022708905.1_ASM2270890v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 07:32:17,032] [INFO] Task succeeded: Prodigal
[2023-06-13 07:32:17,033] [INFO] Task started: HMMsearch
[2023-06-13 07:32:17,033] [INFO] Running command: hmmsearch --tblout GCA_022708905.1_ASM2270890v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86c48cdc-adda-4feb-b812-4f369bc36a2f/dqc_reference/reference_markers.hmm GCA_022708905.1_ASM2270890v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 07:32:17,272] [INFO] Task succeeded: HMMsearch
[2023-06-13 07:32:17,274] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9152f558-e8c0-4bcf-a8e9-ce618451b6c5/GCA_022708905.1_ASM2270890v1_genomic.fna.gz]
[2023-06-13 07:32:17,299] [INFO] Query marker FASTA was written to GCA_022708905.1_ASM2270890v1_genomic.fna/markers.fasta
[2023-06-13 07:32:17,300] [INFO] Task started: Blastn
[2023-06-13 07:32:17,300] [INFO] Running command: blastn -query GCA_022708905.1_ASM2270890v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86c48cdc-adda-4feb-b812-4f369bc36a2f/dqc_reference/reference_markers.fasta -out GCA_022708905.1_ASM2270890v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 07:32:18,022] [INFO] Task succeeded: Blastn
[2023-06-13 07:32:18,026] [INFO] Selected 23 target genomes.
[2023-06-13 07:32:18,026] [INFO] Target genome list was writen to GCA_022708905.1_ASM2270890v1_genomic.fna/target_genomes.txt
[2023-06-13 07:32:18,035] [INFO] Task started: fastANI
[2023-06-13 07:32:18,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg9152f558-e8c0-4bcf-a8e9-ce618451b6c5/GCA_022708905.1_ASM2270890v1_genomic.fna.gz --refList GCA_022708905.1_ASM2270890v1_genomic.fna/target_genomes.txt --output GCA_022708905.1_ASM2270890v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 07:32:40,702] [INFO] Task succeeded: fastANI
[2023-06-13 07:32:40,703] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86c48cdc-adda-4feb-b812-4f369bc36a2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 07:32:40,703] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86c48cdc-adda-4feb-b812-4f369bc36a2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 07:32:40,721] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 07:32:40,721] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 07:32:40,721] [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 sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	77.0404	60	460	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.9348	83	460	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.6107	110	460	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.1498	68	460	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	76.0474	65	460	95	below_threshold
Nonomuraea typhae	strain=p1410	GCA_009760925.1	2603600	2603600	type	True	75.5453	57	460	95	below_threshold
Microtetraspora niveoalba	strain=NBRC 15239	GCA_001570405.1	46175	46175	type	True	75.3356	65	460	95	below_threshold
Actinomadura kijaniata	strain=NBRC 14229	GCA_001552175.1	46161	46161	type	True	75.3109	75	460	95	below_threshold
Pseudonocardia broussonetiae	strain=Gen 01	GCA_013155125.1	2736640	2736640	type	True	75.3075	62	460	95	below_threshold
Actinomadura namibiensis	strain=DSM 44197	GCA_014138665.1	182080	182080	type	True	75.2542	72	460	95	below_threshold
Asanoa siamensis	strain=NBRC 107932	GCA_016862555.1	926357	926357	type	True	75.1969	58	460	95	below_threshold
Actinomadura decatromicini	strain=CYP1-5	GCA_008121305.1	2604572	2604572	type	True	75.1936	76	460	95	below_threshold
Actinomadura geliboluensis	strain=A8036	GCA_005889745.1	882440	882440	type	True	75.1832	72	460	95	below_threshold
Actinophytocola algeriensis	strain=CECT 8960	GCA_014203735.1	1768010	1768010	type	True	75.1697	69	460	95	below_threshold
Streptomyces cahuitamycinicus	strain=13K301	GCA_002891435.1	2070367	2070367	type	True	75.1681	57	460	95	below_threshold
Actinophytocola algeriensis	strain=DSM 46746	GCA_014874055.1	1768010	1768010	type	True	75.1509	71	460	95	below_threshold
Conexibacter arvalis	strain=DSM 23288	GCA_014199525.1	912552	912552	type	True	75.1278	65	460	95	below_threshold
Micromonospora krabiensis	strain=DSM 45344	GCA_900091425.1	307121	307121	type	True	75.0026	56	460	95	below_threshold
Micromonospora zamorensis	strain=DSM 45600	GCA_900090275.1	709883	709883	type	True	74.8388	51	460	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 07:32:40,724] [INFO] DFAST Taxonomy check result was written to GCA_022708905.1_ASM2270890v1_genomic.fna/tc_result.tsv
[2023-06-13 07:32:40,724] [INFO] ===== Taxonomy check completed =====
[2023-06-13 07:32:40,724] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 07:32:40,725] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86c48cdc-adda-4feb-b812-4f369bc36a2f/dqc_reference/checkm_data
[2023-06-13 07:32:40,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 07:32:40,756] [INFO] Task started: CheckM
[2023-06-13 07:32:40,756] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708905.1_ASM2270890v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708905.1_ASM2270890v1_genomic.fna/checkm_input GCA_022708905.1_ASM2270890v1_genomic.fna/checkm_result
[2023-06-13 07:33:03,581] [INFO] Task succeeded: CheckM
[2023-06-13 07:33:03,582] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 53.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 07:33:03,603] [INFO] ===== Completeness check finished =====
[2023-06-13 07:33:03,603] [INFO] ===== Start GTDB Search =====
[2023-06-13 07:33:03,604] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708905.1_ASM2270890v1_genomic.fna/markers.fasta)
[2023-06-13 07:33:03,604] [INFO] Task started: Blastn
[2023-06-13 07:33:03,604] [INFO] Running command: blastn -query GCA_022708905.1_ASM2270890v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86c48cdc-adda-4feb-b812-4f369bc36a2f/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708905.1_ASM2270890v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 07:33:04,828] [INFO] Task succeeded: Blastn
[2023-06-13 07:33:04,834] [INFO] Selected 17 target genomes.
[2023-06-13 07:33:04,834] [INFO] Target genome list was writen to GCA_022708905.1_ASM2270890v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 07:33:04,934] [INFO] Task started: fastANI
[2023-06-13 07:33:04,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg9152f558-e8c0-4bcf-a8e9-ce618451b6c5/GCA_022708905.1_ASM2270890v1_genomic.fna.gz --refList GCA_022708905.1_ASM2270890v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708905.1_ASM2270890v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 07:33:16,251] [INFO] Task succeeded: fastANI
[2023-06-13 07:33:16,267] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 07:33:16,268] [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_003962875.1	s__AWTP1-35 sp003962875	80.7701	224	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__AWTP1-35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268735.1	s__AWTP1-35 sp018268735	78.8855	145	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__AWTP1-35	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903941145.1	s__CAJANQ01 sp903941145	78.1246	99	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAJANQ01	95.0	98.35	98.35	0.80	0.80	2	-
GCA_903868545.1	s__CAIPVR01 sp903868545	78.0854	165	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__CAIPVR01	95.0	99.51	99.50	0.87	0.86	3	-
GCA_007118345.1	s__SKRR01 sp007118345	77.7597	123	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SKRR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903852755.1	s__SXMI01 sp903852755	77.6292	122	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	99.71	99.61	0.93	0.92	10	-
GCA_016702505.1	s__JAAZBK01 sp016702505	77.5419	69	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JAAYBP01;g__JAAZBK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873135.1	s__SXMI01 sp903873135	77.3236	126	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	99.54	99.49	0.91	0.89	9	-
GCA_903925745.1	s__SXMI01 sp903925745	77.2997	115	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Microtrichaceae;g__SXMI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716005.1	s__JADJXE01 sp016716005	76.2159	90	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__JADJXE01;g__JADJXE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016870475.1	s__VGBO01 sp016870475	76.1235	63	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__CAIXPF01;g__VGBO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016700055.1	s__Kalu-18 sp016700055	75.9361	70	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Kalu-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007122945.1	s__SKSP01 sp007122945	75.9199	78	460	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	99.05	99.05	0.83	0.83	2	-
GCF_900091425.1	s__Micromonospora krabiensis	75.0105	55	460	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862315.1	s__Actinoplanes palleronii	74.9231	67	460	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	97.70	97.70	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-06-13 07:33:16,270] [INFO] GTDB search result was written to GCA_022708905.1_ASM2270890v1_genomic.fna/result_gtdb.tsv
[2023-06-13 07:33:16,270] [INFO] ===== GTDB Search completed =====
[2023-06-13 07:33:16,274] [INFO] DFAST_QC result json was written to GCA_022708905.1_ASM2270890v1_genomic.fna/dqc_result.json
[2023-06-13 07:33:16,275] [INFO] DFAST_QC completed!
[2023-06-13 07:33:16,275] [INFO] Total running time: 0h1m6s