[2024-01-25 17:44:35,486] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:44:35,488] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:44:35,488] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9e7b2f1-60cb-4b4a-ad79-23ce49a6755c/dqc_reference
[2024-01-25 17:44:36,597] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:44:36,598] [INFO] Task started: Prodigal
[2024-01-25 17:44:36,598] [INFO] Running command: gunzip -c /var/lib/cwl/stg196dde3c-e53a-4b6e-a1f0-0d98782b4409/GCF_009735685.1_ASM973568v1_genomic.fna.gz | prodigal -d GCF_009735685.1_ASM973568v1_genomic.fna/cds.fna -a GCF_009735685.1_ASM973568v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:44:53,119] [INFO] Task succeeded: Prodigal
[2024-01-25 17:44:53,120] [INFO] Task started: HMMsearch
[2024-01-25 17:44:53,120] [INFO] Running command: hmmsearch --tblout GCF_009735685.1_ASM973568v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9e7b2f1-60cb-4b4a-ad79-23ce49a6755c/dqc_reference/reference_markers.hmm GCF_009735685.1_ASM973568v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:44:53,389] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:44:53,390] [INFO] Found 6/6 markers.
[2024-01-25 17:44:53,449] [INFO] Query marker FASTA was written to GCF_009735685.1_ASM973568v1_genomic.fna/markers.fasta
[2024-01-25 17:44:53,449] [INFO] Task started: Blastn
[2024-01-25 17:44:53,449] [INFO] Running command: blastn -query GCF_009735685.1_ASM973568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9e7b2f1-60cb-4b4a-ad79-23ce49a6755c/dqc_reference/reference_markers.fasta -out GCF_009735685.1_ASM973568v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:54,717] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:54,721] [INFO] Selected 23 target genomes.
[2024-01-25 17:44:54,722] [INFO] Target genome list was writen to GCF_009735685.1_ASM973568v1_genomic.fna/target_genomes.txt
[2024-01-25 17:44:54,739] [INFO] Task started: fastANI
[2024-01-25 17:44:54,739] [INFO] Running command: fastANI --query /var/lib/cwl/stg196dde3c-e53a-4b6e-a1f0-0d98782b4409/GCF_009735685.1_ASM973568v1_genomic.fna.gz --refList GCF_009735685.1_ASM973568v1_genomic.fna/target_genomes.txt --output GCF_009735685.1_ASM973568v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:45:33,187] [INFO] Task succeeded: fastANI
[2024-01-25 17:45:33,188] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9e7b2f1-60cb-4b4a-ad79-23ce49a6755c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:45:33,188] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9e7b2f1-60cb-4b4a-ad79-23ce49a6755c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:45:33,202] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:45:33,202] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:45:33,202] [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 lycii	strain=TRM 66187	GCA_009735685.1	2654337	2654337	type	True	100.0	2316	2338	95	conclusive
Streptomyces xinghaiensis	strain=S187	GCA_000220705.2	1038928	1038928	type	True	83.4501	1394	2338	95	below_threshold
Streptomyces pathocidini	strain=NRRL B-24287	GCA_001418495.1	1650571	1650571	type	True	82.63	854	2338	95	below_threshold
Streptomyces eurocidicus	strain=CECT 3259	GCA_014203505.1	66423	66423	type	True	81.2327	1097	2338	95	below_threshold
Streptomyces eurocidicus	strain=ATCC 27428	GCA_002891295.1	66423	66423	type	True	81.2213	1084	2338	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	81.1954	1077	2338	95	below_threshold
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	81.1841	1069	2338	95	below_threshold
Streptomyces kronopolitis	strain=CGMCC 4.7323	GCA_014646275.1	1612435	1612435	type	True	81.1658	1130	2338	95	below_threshold
Streptomyces eurocidicus	strain=NRRL ISP-5604	GCA_015475845.1	66423	66423	type	True	81.1568	1119	2338	95	below_threshold
Streptomyces albospinus	strain=JCM 3399	GCA_014648695.1	285515	285515	type	True	81.107	1119	2338	95	below_threshold
Streptomyces pactum	strain=ATCC 27456	GCA_016031615.1	68249	68249	type	True	80.8903	1170	2338	95	below_threshold
Streptomyces libani subsp. libani	strain=NBRC 13452	GCA_009811595.1	68044	68043	type	True	80.8656	1160	2338	95	below_threshold
Streptomyces huiliensis	strain=SCA2-4	GCA_020037025.1	2876027	2876027	type	True	80.8586	1008	2338	95	below_threshold
Streptomyces libani subsp. libani	strain=JCM 4322	GCA_014649275.1	68044	68043	type	True	80.8505	1178	2338	95	below_threshold
Streptomyces sennicomposti	strain=RCPT1-4	GCA_019890635.1	2873384	2873384	type	True	80.8389	1106	2338	95	below_threshold
Streptomyces rapamycinicus	strain=NRRL 5491	GCA_024298965.1	1226757	1226757	type	True	80.7414	1305	2338	95	below_threshold
Streptomyces galbus	strain=JCM 4639	GCA_014650535.1	33898	33898	type	True	80.573	1160	2338	95	below_threshold
Streptomyces galbus	strain=DSM 40089	GCA_005280195.1	33898	33898	type	True	80.5466	1164	2338	95	below_threshold
Streptomyces hirsutus	strain=NRRL B-2713	GCA_001418415.1	35620	35620	type	True	80.5251	1034	2338	95	below_threshold
Streptomyces physcomitrii	strain=LD120	GCA_012273655.1	2724184	2724184	type	True	80.503	1120	2338	95	below_threshold
Streptomyces rubrisoli	strain=DSM 42083	GCA_024436055.1	1387313	1387313	type	True	80.4735	926	2338	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	80.2508	1131	2338	95	below_threshold
Streptomyces dysideae	strain=RV15	GCA_001514305.1	909626	909626	type	True	80.017	1207	2338	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:45:33,204] [INFO] DFAST Taxonomy check result was written to GCF_009735685.1_ASM973568v1_genomic.fna/tc_result.tsv
[2024-01-25 17:45:33,204] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:45:33,204] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:45:33,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9e7b2f1-60cb-4b4a-ad79-23ce49a6755c/dqc_reference/checkm_data
[2024-01-25 17:45:33,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:45:33,290] [INFO] Task started: CheckM
[2024-01-25 17:45:33,290] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009735685.1_ASM973568v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009735685.1_ASM973568v1_genomic.fna/checkm_input GCF_009735685.1_ASM973568v1_genomic.fna/checkm_result
[2024-01-25 17:47:02,598] [INFO] Task succeeded: CheckM
[2024-01-25 17:47:02,599] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:47:02,620] [INFO] ===== Completeness check finished =====
[2024-01-25 17:47:02,620] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:47:02,621] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009735685.1_ASM973568v1_genomic.fna/markers.fasta)
[2024-01-25 17:47:02,621] [INFO] Task started: Blastn
[2024-01-25 17:47:02,621] [INFO] Running command: blastn -query GCF_009735685.1_ASM973568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9e7b2f1-60cb-4b4a-ad79-23ce49a6755c/dqc_reference/reference_markers_gtdb.fasta -out GCF_009735685.1_ASM973568v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:47:04,791] [INFO] Task succeeded: Blastn
[2024-01-25 17:47:04,793] [INFO] Selected 12 target genomes.
[2024-01-25 17:47:04,793] [INFO] Target genome list was writen to GCF_009735685.1_ASM973568v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:47:04,813] [INFO] Task started: fastANI
[2024-01-25 17:47:04,813] [INFO] Running command: fastANI --query /var/lib/cwl/stg196dde3c-e53a-4b6e-a1f0-0d98782b4409/GCF_009735685.1_ASM973568v1_genomic.fna.gz --refList GCF_009735685.1_ASM973568v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009735685.1_ASM973568v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:47:26,409] [INFO] Task succeeded: fastANI
[2024-01-25 17:47:26,417] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:47:26,417] [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_002573955.1	s__Streptomyces sp002573955	99.2072	1952	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.25	99.25	0.87	0.87	2	conclusive
GCA_003519485.1	s__Streptomyces sp003519485	84.5364	866	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719865.1	s__Streptomyces albus_E	83.488	1322	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220705.2	s__Streptomyces xinghaiensis	83.4535	1395	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.52	96.44	0.86	0.81	7	-
GCF_018070345.1	s__Streptomyces sp018070345	83.1602	1322	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012034935.1	s__Streptomyces sp012034935	82.1745	1252	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002154585.1	s__Streptomyces pseudogriseolus	81.0178	1023	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.58	96.58	0.90	0.87	9	-
GCF_016031615.1	s__Streptomyces pactum	80.8854	1170	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002082195.1	s__Streptomyces gilvosporeus	80.8636	1082	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0251	N/A	N/A	N/A	N/A	1	-
GCF_000424825.1	s__Streptomyces sp000424825	80.5502	1008	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003261055.1	s__Streptomyces cadmiisoli	80.3229	1184	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.22	99.22	0.88	0.88	2	-
GCF_000426165.1	s__Streptomyces sp000426165	79.8681	962	2338	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:47:26,418] [INFO] GTDB search result was written to GCF_009735685.1_ASM973568v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:47:26,419] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:47:26,423] [INFO] DFAST_QC result json was written to GCF_009735685.1_ASM973568v1_genomic.fna/dqc_result.json
[2024-01-25 17:47:26,423] [INFO] DFAST_QC completed!
[2024-01-25 17:47:26,423] [INFO] Total running time: 0h2m51s