[2024-01-24 13:49:45,348] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:45,350] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:45,350] [INFO] DQC Reference Directory: /var/lib/cwl/stg9578cf87-5595-400e-a47c-35bbb2a8328e/dqc_reference
[2024-01-24 13:49:46,663] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:46,663] [INFO] Task started: Prodigal
[2024-01-24 13:49:46,664] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0a1996d-4c88-4aa2-9394-b483970ec073/GCF_011044975.1_ASM1104497v1_genomic.fna.gz | prodigal -d GCF_011044975.1_ASM1104497v1_genomic.fna/cds.fna -a GCF_011044975.1_ASM1104497v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:10,400] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:10,400] [INFO] Task started: HMMsearch
[2024-01-24 13:50:10,401] [INFO] Running command: hmmsearch --tblout GCF_011044975.1_ASM1104497v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9578cf87-5595-400e-a47c-35bbb2a8328e/dqc_reference/reference_markers.hmm GCF_011044975.1_ASM1104497v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:10,788] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:10,789] [INFO] Found 6/6 markers.
[2024-01-24 13:50:10,858] [INFO] Query marker FASTA was written to GCF_011044975.1_ASM1104497v1_genomic.fna/markers.fasta
[2024-01-24 13:50:10,859] [INFO] Task started: Blastn
[2024-01-24 13:50:10,859] [INFO] Running command: blastn -query GCF_011044975.1_ASM1104497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9578cf87-5595-400e-a47c-35bbb2a8328e/dqc_reference/reference_markers.fasta -out GCF_011044975.1_ASM1104497v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:12,207] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:12,210] [INFO] Selected 27 target genomes.
[2024-01-24 13:50:12,210] [INFO] Target genome list was writen to GCF_011044975.1_ASM1104497v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:12,220] [INFO] Task started: fastANI
[2024-01-24 13:50:12,220] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0a1996d-4c88-4aa2-9394-b483970ec073/GCF_011044975.1_ASM1104497v1_genomic.fna.gz --refList GCF_011044975.1_ASM1104497v1_genomic.fna/target_genomes.txt --output GCF_011044975.1_ASM1104497v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:57,438] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:57,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9578cf87-5595-400e-a47c-35bbb2a8328e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:57,439] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9578cf87-5595-400e-a47c-35bbb2a8328e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:57,460] [INFO] Found 27 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:57,460] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:57,460] [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
Streptomyces coryli	strain=A7024	GCA_011044975.1	1128680	1128680	type	True	100.0	2698	2721	95	conclusive
Streptomyces pathocidini	strain=NRRL B-24287	GCA_001418495.1	1650571	1650571	type	True	80.96	839	2721	95	below_threshold
Streptomyces smaragdinus	strain=RB5	GCA_009604385.1	2585196	2585196	type	True	80.8539	1190	2721	95	below_threshold
Streptomyces chryseus	strain=DSM 40420	GCA_005981935.1	68186	68186	type	True	80.586	885	2721	95	below_threshold
Streptomyces albidochromogenes	strain=DSM 41800	GCA_005981925.1	329524	329524	type	True	80.3513	1005	2721	95	below_threshold
Streptomyces mesophilus	strain=YC504	GCA_011044995.1	1775132	1775132	type	True	80.3232	1233	2721	95	below_threshold
Streptomyces chryseus	strain=JCM 4737	GCA_014650755.1	68186	68186	type	True	80.1757	1102	2721	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	80.1194	1095	2721	95	below_threshold
Streptomyces benahoarensis	strain=MZ03-37	GCA_007280575.1	2595054	2595054	type	True	80.055	914	2721	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002843305.1	1257026	1257026	type	True	80.0199	963	2721	95	below_threshold
Streptomyces curacoi	strain=DSM 40107	GCA_001513975.1	146536	146536	type	True	80.011	1223	2721	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	79.9794	1244	2721	95	below_threshold
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	79.9652	939	2721	95	below_threshold
Streptomyces longwoodensis	strain=DSM 41677	GCA_001514125.1	68231	68231	type	True	79.9462	1194	2721	95	below_threshold
Streptomyces barkulensis	strain=RC 1831	GCA_002811705.2	1257026	1257026	type	True	79.8898	973	2721	95	below_threshold
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	79.8535	1174	2721	95	below_threshold
Streptomyces albireticuli	strain=NRRL B1670	GCA_021228125.1	1940	1940	type	True	79.8238	1090	2721	95	below_threshold
Streptomyces spectabilis	strain=ATCC 27465	GCA_008704795.1	68270	68270	type	True	79.8219	1304	2721	95	below_threshold
Streptomyces rubradiris	strain=NBRC 14000	GCA_016860525.1	285531	285531	type	True	79.7813	1201	2721	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	79.7506	1323	2721	95	below_threshold
Streptomyces spectabilis	strain=JCM 4308	GCA_014649235.1	68270	68270	type	True	79.747	1313	2721	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	79.7462	1185	2721	95	below_threshold
Streptomyces alkaliterrae	strain=OF1	GCA_007097205.2	2213162	2213162	type	True	79.7144	810	2721	95	below_threshold
Streptomyces justiciae	strain=3R004	GCA_015163075.1	2780140	2780140	type	True	79.6826	1271	2721	95	below_threshold
Streptomyces buecherae	strain=AC541	GCA_014295035.1	2763006	2763006	type	True	79.6722	1134	2721	95	below_threshold
Streptomyces yatensis	strain=DSM 41771	GCA_018069625.1	155177	155177	type	True	79.6417	1276	2721	95	below_threshold
Actinacidiphila glaucinigra	strain=CGMCC 4.1858	GCA_900188405.1	235986	235986	type	True	79.5205	1171	2721	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:57,462] [INFO] DFAST Taxonomy check result was written to GCF_011044975.1_ASM1104497v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:57,462] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:57,463] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:57,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9578cf87-5595-400e-a47c-35bbb2a8328e/dqc_reference/checkm_data
[2024-01-24 13:50:57,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:57,550] [INFO] Task started: CheckM
[2024-01-24 13:50:57,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011044975.1_ASM1104497v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011044975.1_ASM1104497v1_genomic.fna/checkm_input GCF_011044975.1_ASM1104497v1_genomic.fna/checkm_result
[2024-01-24 13:52:05,590] [INFO] Task succeeded: CheckM
[2024-01-24 13:52:05,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.12%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 13:52:05,620] [INFO] ===== Completeness check finished =====
[2024-01-24 13:52:05,620] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:52:05,621] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011044975.1_ASM1104497v1_genomic.fna/markers.fasta)
[2024-01-24 13:52:05,621] [INFO] Task started: Blastn
[2024-01-24 13:52:05,621] [INFO] Running command: blastn -query GCF_011044975.1_ASM1104497v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9578cf87-5595-400e-a47c-35bbb2a8328e/dqc_reference/reference_markers_gtdb.fasta -out GCF_011044975.1_ASM1104497v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:52:07,763] [INFO] Task succeeded: Blastn
[2024-01-24 13:52:07,767] [INFO] Selected 25 target genomes.
[2024-01-24 13:52:07,768] [INFO] Target genome list was writen to GCF_011044975.1_ASM1104497v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:52:07,835] [INFO] Task started: fastANI
[2024-01-24 13:52:07,836] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0a1996d-4c88-4aa2-9394-b483970ec073/GCF_011044975.1_ASM1104497v1_genomic.fna.gz --refList GCF_011044975.1_ASM1104497v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011044975.1_ASM1104497v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:52:53,404] [INFO] Task succeeded: fastANI
[2024-01-24 13:52:53,429] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:52:53,430] [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_011044975.1	s__Streptomyces sp011044975	100.0	2698	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000514715.1	s__Streptomyces sp000514715	80.9824	1367	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797655.1	s__Streptomyces sp002797655	80.8872	1415	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.99	97.30	0.92	0.88	9	-
GCF_009604385.1	s__Streptomyces sp009604385	80.8595	1192	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002847285.1	s__Streptomyces sp002847285	80.7224	1371	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.16	95.03	0.85	0.85	4	-
GCF_000482585.1	s__Streptomyces sp000482585	80.6413	1276	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005981925.1	s__Streptomyces albidochromogenes	80.3717	1001	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.5104	N/A	N/A	N/A	N/A	1	-
GCF_003945545.1	s__Streptomyces sp003945545	80.2246	1203	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007280575.1	s__Streptomyces sp007280575	80.092	908	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746415.1	s__Streptomyces agglomeratus	80.0441	1114	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.50	99.39	0.92	0.91	5	-
GCF_001513975.1	s__Streptomyces curacoi	80.03	1219	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.35	97.22	0.89	0.84	4	-
GCF_002843305.1	s__Streptomyces barkulensis	79.9874	970	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	96.765	99.92	99.92	0.99	0.99	2	-
GCF_007595705.1	s__Streptomyces sp007595705	79.9822	1110	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014650875.1	s__Streptomyces minutiscleroticus	79.9804	1245	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	98.56	0.90	0.90	2	-
GCF_001514125.1	s__Streptomyces longwoodensis	79.9676	1188	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.95	95.95	0.86	0.86	2	-
GCF_004684805.1	s__Streptomyces palmae	79.8889	952	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011045025.1	s__Streptomyces ureilyticus	79.8658	1136	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704795.1	s__Streptomyces spectabilis	79.8481	1298	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.73	96.21	0.96	0.90	4	-
GCF_005280195.1	s__Streptomyces galbus	79.8137	1181	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.26	98.53	0.96	0.94	3	-
GCF_007097205.2	s__Streptomyces alkaliterrae	79.7453	805	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.63	99.32	0.91	0.86	3	-
GCF_014649375.1	s__Streptomyces aurantiogriseus	79.7288	1247	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222485.1	s__Streptomyces griseoviridis_A	79.701	1205	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014295035.1	s__Streptomyces buecherae	79.621	1144	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.71	96.93	0.96	0.94	7	-
GCF_900188405.1	s__Streptomyces glauciniger	79.5086	1174	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.09	95.09	0.86	0.86	3	-
GCA_018114805.1	s__Streptomyces philanthi	79.413	1001	2721	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:52:53,431] [INFO] GTDB search result was written to GCF_011044975.1_ASM1104497v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:52:53,432] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:52:53,437] [INFO] DFAST_QC result json was written to GCF_011044975.1_ASM1104497v1_genomic.fna/dqc_result.json
[2024-01-24 13:52:53,437] [INFO] DFAST_QC completed!
[2024-01-24 13:52:53,437] [INFO] Total running time: 0h3m8s