[2024-01-24 13:36:45,685] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:45,689] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:45,689] [INFO] DQC Reference Directory: /var/lib/cwl/stg3ea6f948-a56d-43c5-a789-572da8043541/dqc_reference
[2024-01-24 13:36:46,992] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:36:46,993] [INFO] Task started: Prodigal
[2024-01-24 13:36:46,993] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb830991-e430-48df-9ebc-32468183ea25/GCF_022647665.1_ASM2264766v1_genomic.fna.gz | prodigal -d GCF_022647665.1_ASM2264766v1_genomic.fna/cds.fna -a GCF_022647665.1_ASM2264766v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:12,030] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:12,031] [INFO] Task started: HMMsearch
[2024-01-24 13:37:12,031] [INFO] Running command: hmmsearch --tblout GCF_022647665.1_ASM2264766v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3ea6f948-a56d-43c5-a789-572da8043541/dqc_reference/reference_markers.hmm GCF_022647665.1_ASM2264766v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:12,498] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:12,499] [INFO] Found 6/6 markers.
[2024-01-24 13:37:12,564] [INFO] Query marker FASTA was written to GCF_022647665.1_ASM2264766v1_genomic.fna/markers.fasta
[2024-01-24 13:37:12,564] [INFO] Task started: Blastn
[2024-01-24 13:37:12,565] [INFO] Running command: blastn -query GCF_022647665.1_ASM2264766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ea6f948-a56d-43c5-a789-572da8043541/dqc_reference/reference_markers.fasta -out GCF_022647665.1_ASM2264766v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:13,972] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:13,976] [INFO] Selected 21 target genomes.
[2024-01-24 13:37:13,976] [INFO] Target genome list was writen to GCF_022647665.1_ASM2264766v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:13,987] [INFO] Task started: fastANI
[2024-01-24 13:37:13,987] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb830991-e430-48df-9ebc-32468183ea25/GCF_022647665.1_ASM2264766v1_genomic.fna.gz --refList GCF_022647665.1_ASM2264766v1_genomic.fna/target_genomes.txt --output GCF_022647665.1_ASM2264766v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:57,293] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:57,293] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3ea6f948-a56d-43c5-a789-572da8043541/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:57,294] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3ea6f948-a56d-43c5-a789-572da8043541/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:57,310] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:57,310] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:57,310] [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 formicae	strain=1H-GS9	GCA_022647665.1	1616117	1616117	type	True	100.0	2729	2734	95	conclusive
Streptomyces wuyuanensis	strain=CGMCC 4.7042	GCA_900103455.1	1196353	1196353	type	True	85.418	1719	2734	95	below_threshold
Streptomyces tirandamycinicus	strain=HNM0039	GCA_003097515.1	2174846	2174846	type	True	85.0297	1577	2734	95	below_threshold
Streptomyces marianii	strain=ICN19	GCA_005795905.1	1817406	1817406	type	True	85.0151	1656	2734	95	below_threshold
Streptomyces spongiicola	strain=HNM0071	GCA_003122365.1	1690221	1690221	type	True	84.4326	1500	2734	95	below_threshold
Streptomyces lunaelactis	strain=MM109	GCA_003054555.1	1535768	1535768	type	True	84.1854	1567	2734	95	below_threshold
Streptomyces purpureus	strain=JCM 3172	GCA_014648195.1	1951	1951	type	True	83.9947	1476	2734	95	below_threshold
Streptomyces lavendofoliae	strain=JCM 4391	GCA_014649735.1	67314	67314	type	True	83.7544	1392	2734	95	below_threshold
Streptomyces nashvillensis	strain=JCM 4498	GCA_014650095.1	67334	67334	type	True	83.247	1485	2734	95	below_threshold
Streptomyces melanogenes	strain=JCM 4398	GCA_014649795.1	67326	67326	type	True	83.1477	1480	2734	95	below_threshold
Streptomyces genisteinicus	strain=CRPJ-33	GCA_014489615.1	2768068	2768068	type	True	83.0939	1450	2734	95	below_threshold
Streptomyces sudanensis	strain=SD 504	GCA_023614315.1	436397	436397	type	True	82.6915	1086	2734	95	below_threshold
Streptomyces lichenis	strain=LCR6-01	GCA_023218175.1	2306967	2306967	type	True	82.4852	1362	2734	95	below_threshold
Streptomyces minutiscleroticus	strain=JCM 4790	GCA_014650875.1	68238	68238	type	True	82.1676	1385	2734	95	below_threshold
Streptomyces lomondensis	strain=JCM 4866	GCA_014651035.1	68229	68229	type	True	81.9828	1443	2734	95	below_threshold
Streptomyces lomondensis	strain=DSM 41428	GCA_021440105.1	68229	68229	type	True	81.9555	1445	2734	95	below_threshold
Streptomyces spiralis	strain=JCM 3302	GCA_014654675.1	66376	66376	type	True	81.7438	1397	2734	95	below_threshold
Streptomyces barringtoniae	strain=JA03	GCA_020819595.1	2892029	2892029	type	True	81.7085	1397	2734	95	below_threshold
Streptomyces mangrovisoli	strain=MUSC 149	GCA_000974985.2	1428628	1428628	type	True	81.6792	1361	2734	95	below_threshold
Streptomyces brasiliensis	strain=JCM 3086	GCA_014647875.1	1954	1954	type	True	81.3566	1425	2734	95	below_threshold
Streptacidiphilus melanogenes	strain=NBRC 103184	GCA_000787835.1	411235	411235	type	True	78.7646	933	2734	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:57,312] [INFO] DFAST Taxonomy check result was written to GCF_022647665.1_ASM2264766v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:57,312] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:57,313] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:57,313] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3ea6f948-a56d-43c5-a789-572da8043541/dqc_reference/checkm_data
[2024-01-24 13:37:57,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:57,394] [INFO] Task started: CheckM
[2024-01-24 13:37:57,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022647665.1_ASM2264766v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022647665.1_ASM2264766v1_genomic.fna/checkm_input GCF_022647665.1_ASM2264766v1_genomic.fna/checkm_result
[2024-01-24 13:40:03,046] [INFO] Task succeeded: CheckM
[2024-01-24 13:40:03,048] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:40:03,079] [INFO] ===== Completeness check finished =====
[2024-01-24 13:40:03,079] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:40:03,080] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022647665.1_ASM2264766v1_genomic.fna/markers.fasta)
[2024-01-24 13:40:03,080] [INFO] Task started: Blastn
[2024-01-24 13:40:03,081] [INFO] Running command: blastn -query GCF_022647665.1_ASM2264766v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3ea6f948-a56d-43c5-a789-572da8043541/dqc_reference/reference_markers_gtdb.fasta -out GCF_022647665.1_ASM2264766v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:05,144] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:05,148] [INFO] Selected 25 target genomes.
[2024-01-24 13:40:05,148] [INFO] Target genome list was writen to GCF_022647665.1_ASM2264766v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:40:05,218] [INFO] Task started: fastANI
[2024-01-24 13:40:05,218] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb830991-e430-48df-9ebc-32468183ea25/GCF_022647665.1_ASM2264766v1_genomic.fna.gz --refList GCF_022647665.1_ASM2264766v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022647665.1_ASM2264766v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:40:52,726] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:52,751] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:40:52,752] [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_900103455.1	s__Streptomyces wuyuanensis	85.397	1722	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003097515.1	s__Streptomyces tirandamycinicus	85.0164	1575	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.65	98.27	0.90	0.88	6	-
GCF_005795905.1	s__Streptomyces marianii	85.0125	1655	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003725745.1	s__Streptomyces sp003725745	84.7861	1563	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122365.1	s__Streptomyces spongiicola	84.4605	1494	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.39	99.39	0.96	0.96	2	-
GCF_001905885.1	s__Streptomyces sp001905885	84.2209	1537	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	96.05	96.05	0.87	0.87	2	-
GCF_003054555.1	s__Streptomyces lunaelactis	84.1513	1573	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.21	97.91	0.90	0.85	18	-
GCF_011766325.1	s__Streptomyces sp011766325	84.0743	1387	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004353505.1	s__Streptomyces sp004353505	84.0169	1458	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.95	99.86	0.97	0.92	4	-
GCF_014648195.1	s__Streptomyces purpureus	84.0005	1474	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.54	99.54	0.95	0.95	2	-
GCF_001646665.1	s__Streptomyces albulus_A	83.9371	1433	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649735.1	s__Streptomyces lavendofoliae	83.7242	1395	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000716335.1	s__Streptomyces sp000716335	83.7015	1465	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001653515.1	s__Streptomyces sp001653515	83.1913	1247	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001905665.1	s__Streptomyces sp001905665	83.1678	1433	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014649795.1	s__Streptomyces melanogenes	83.1655	1479	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.19	95.19	0.83	0.83	2	-
GCF_008271805.1	s__Streptomyces sp008271805	83.1439	1320	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100315.1	s__Streptomyces indicus	82.2161	1378	2734	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	82.1829	1384	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.56	98.56	0.90	0.90	2	-
GCF_014654675.1	s__Streptomyces spiralis	81.7331	1398	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.07	98.07	0.87	0.87	2	-
GCF_009604455.1	s__Streptomyces sp009604455	81.6512	1418	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103585.1	s__Streptomyces sp900103585	81.6266	1504	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014647875.1	s__Streptomyces brasiliensis	81.3807	1420	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018138715.1	s__Streptomyces asiaticus	80.8965	1372	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	98.17	95.36	0.90	0.81	10	-
GCF_000787835.1	s__Streptacidiphilus melanogenes	78.7887	933	2734	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptacidiphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:40:52,754] [INFO] GTDB search result was written to GCF_022647665.1_ASM2264766v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:40:52,754] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:40:52,759] [INFO] DFAST_QC result json was written to GCF_022647665.1_ASM2264766v1_genomic.fna/dqc_result.json
[2024-01-24 13:40:52,760] [INFO] DFAST_QC completed!
[2024-01-24 13:40:52,760] [INFO] Total running time: 0h4m7s