[2024-01-24 14:22:33,234] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:33,240] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:33,240] [INFO] DQC Reference Directory: /var/lib/cwl/stg95b1065b-ac64-4003-bde7-872ac4e8b6d6/dqc_reference
[2024-01-24 14:22:34,558] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:34,559] [INFO] Task started: Prodigal
[2024-01-24 14:22:34,559] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a58efa6-c7a5-4c85-a037-a4f841bbbc84/GCF_900155595.1_PRJEB18043_genomic.fna.gz | prodigal -d GCF_900155595.1_PRJEB18043_genomic.fna/cds.fna -a GCF_900155595.1_PRJEB18043_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:41,961] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:41,961] [INFO] Task started: HMMsearch
[2024-01-24 14:22:41,962] [INFO] Running command: hmmsearch --tblout GCF_900155595.1_PRJEB18043_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg95b1065b-ac64-4003-bde7-872ac4e8b6d6/dqc_reference/reference_markers.hmm GCF_900155595.1_PRJEB18043_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:42,230] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:42,232] [INFO] Found 6/6 markers.
[2024-01-24 14:22:42,258] [INFO] Query marker FASTA was written to GCF_900155595.1_PRJEB18043_genomic.fna/markers.fasta
[2024-01-24 14:22:42,258] [INFO] Task started: Blastn
[2024-01-24 14:22:42,259] [INFO] Running command: blastn -query GCF_900155595.1_PRJEB18043_genomic.fna/markers.fasta -db /var/lib/cwl/stg95b1065b-ac64-4003-bde7-872ac4e8b6d6/dqc_reference/reference_markers.fasta -out GCF_900155595.1_PRJEB18043_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:43,223] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:43,229] [INFO] Selected 23 target genomes.
[2024-01-24 14:22:43,230] [INFO] Target genome list was writen to GCF_900155595.1_PRJEB18043_genomic.fna/target_genomes.txt
[2024-01-24 14:22:43,244] [INFO] Task started: fastANI
[2024-01-24 14:22:43,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a58efa6-c7a5-4c85-a037-a4f841bbbc84/GCF_900155595.1_PRJEB18043_genomic.fna.gz --refList GCF_900155595.1_PRJEB18043_genomic.fna/target_genomes.txt --output GCF_900155595.1_PRJEB18043_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:56,131] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:56,132] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg95b1065b-ac64-4003-bde7-872ac4e8b6d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:56,132] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg95b1065b-ac64-4003-bde7-872ac4e8b6d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:56,156] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:22:56,157] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:22:56,157] [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
Schaalia hyovaginalis	strain=DSM 10695	GCA_014208035.1	29316	29316	type	True	80.2067	385	797	95	below_threshold
Schaalia meyeri	strain=DSM 20733	GCA_900105015.1	52773	52773	type	True	78.7418	169	797	95	below_threshold
Schaalia meyeri	strain=FDAARGOS_985	GCA_016127995.1	52773	52773	type	True	78.6762	174	797	95	below_threshold
Actinomyces polynesiensis	strain=MS2	GCA_000820725.1	1325934	1325934	type	True	78.3524	181	797	95	below_threshold
Actinomyces provencensis	strain=SN12	GCA_900155435.1	1720198	1720198	type	True	78.3348	202	797	95	below_threshold
Schaalia vaccimaxillae	strain=DSM 15804	GCA_000420425.1	183916	183916	type	True	77.9419	156	797	95	below_threshold
Actinomyces haliotis	strain=JCM 18848	GCA_015355765.1	1280843	1280843	type	True	77.8309	160	797	95	below_threshold
Actinomyces radicidentis	strain=CCUG 36733	GCA_001553565.1	111015	111015	type	True	77.8304	190	797	95	below_threshold
Actinomyces timonensis	strain=7400942	GCA_000295095.1	1288391	1288391	type	True	77.7977	163	797	95	below_threshold
Actinomyces howellii	strain=Sh 7/4276	GCA_009935825.1	52771	52771	type	True	77.546	137	797	95	below_threshold
Actinomyces slackii	strain=NCTC11923	GCA_900637295.1	52774	52774	type	True	77.4731	141	797	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.388	108	797	95	below_threshold
Actinomyces slackii	strain=ATCC 49928	GCA_000428685.1	52774	52774	type	True	77.3038	141	797	95	below_threshold
Georgenia wutianyii	strain=Z294	GCA_006349365.1	2585135	2585135	type	True	77.2163	127	797	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	77.133	115	797	95	below_threshold
Georgenia subflava	strain=JCM 19765	GCA_009362315.1	1622177	1622177	type	True	77.1156	106	797	95	below_threshold
Georgenia soli	strain=DSM 21838	GCA_002563695.1	638953	638953	type	True	77.0908	123	797	95	below_threshold
Georgenia subflava	strain=CGMCC 1.12782	GCA_009193155.1	1622177	1622177	type	True	76.9087	114	797	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.6717	99	797	95	below_threshold
Gulosibacter faecalis	strain=B187	GCA_000381765.1	272240	272240	type	True	76.0468	59	797	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	75.7895	86	797	95	below_threshold
Streptomyces griseocarneus	strain=CGMCC4.1088	GCA_020093395.1	51201	51201	type	True	75.6791	76	797	95	below_threshold
Streptomyces griseocarneus	strain=JCM 4580	GCA_014655595.1	51201	51201	type	True	75.5272	74	797	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:56,159] [INFO] DFAST Taxonomy check result was written to GCF_900155595.1_PRJEB18043_genomic.fna/tc_result.tsv
[2024-01-24 14:22:56,159] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:56,159] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:56,160] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg95b1065b-ac64-4003-bde7-872ac4e8b6d6/dqc_reference/checkm_data
[2024-01-24 14:22:56,161] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:56,186] [INFO] Task started: CheckM
[2024-01-24 14:22:56,186] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900155595.1_PRJEB18043_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900155595.1_PRJEB18043_genomic.fna/checkm_input GCF_900155595.1_PRJEB18043_genomic.fna/checkm_result
[2024-01-24 14:23:23,963] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:23,965] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:23,987] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:23,988] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:23,988] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900155595.1_PRJEB18043_genomic.fna/markers.fasta)
[2024-01-24 14:23:23,989] [INFO] Task started: Blastn
[2024-01-24 14:23:23,989] [INFO] Running command: blastn -query GCF_900155595.1_PRJEB18043_genomic.fna/markers.fasta -db /var/lib/cwl/stg95b1065b-ac64-4003-bde7-872ac4e8b6d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_900155595.1_PRJEB18043_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:25,468] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:25,472] [INFO] Selected 14 target genomes.
[2024-01-24 14:23:25,472] [INFO] Target genome list was writen to GCF_900155595.1_PRJEB18043_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:25,484] [INFO] Task started: fastANI
[2024-01-24 14:23:25,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a58efa6-c7a5-4c85-a037-a4f841bbbc84/GCF_900155595.1_PRJEB18043_genomic.fna.gz --refList GCF_900155595.1_PRJEB18043_genomic.fna/target_genomes_gtdb.txt --output GCF_900155595.1_PRJEB18043_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:31,946] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:31,963] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:31,963] [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_900155595.1	s__Pauljensenia mediterranea	100.0	797	797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016405145.1	s__Pauljensenia cardiffensis	80.589	290	797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.37	97.30	0.94	0.93	4	-
GCF_900499005.1	s__Pauljensenia culturomici	80.2244	388	797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014208035.1	s__Pauljensenia hyovaginalis	80.2008	385	797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	95.48	95.48	0.88	0.88	2	-
GCF_001746855.1	s__Pauljensenia hongkongensis	79.1634	213	797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	98.51	97.69	0.81	0.72	5	-
GCF_005696695.1	s__Pauljensenia odontolytica_C	79.0798	217	797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.76	95.52	0.95	0.90	3	-
GCF_018986735.1	s__Pauljensenia sp018986735	78.8212	233	797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000411415.1	s__Pauljensenia sp000411415	78.8031	218	797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.95	97.15	0.96	0.94	6	-
GCF_002847525.1	s__Pauljensenia odontolytica_B	78.7824	216	797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	97.06	96.22	0.94	0.92	3	-
GCF_001838165.1	s__Pauljensenia sp001838165	78.6598	224	797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	96.43	95.77	0.94	0.90	5	-
GCA_018382595.1	s__Pauljensenia sp018382595	78.423	206	797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902373435.1	s__Pauljensenia sp902373435	78.3961	185	797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	95.35	95.27	0.85	0.81	3	-
GCF_000820725.1	s__Pauljensenia polynesiensis	78.3524	181	797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	100.00	100.00	0.98	0.98	2	-
GCF_903645355.1	s__Pauljensenia sp903645355	77.9695	139	797	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Pauljensenia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:31,965] [INFO] GTDB search result was written to GCF_900155595.1_PRJEB18043_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:31,965] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:31,970] [INFO] DFAST_QC result json was written to GCF_900155595.1_PRJEB18043_genomic.fna/dqc_result.json
[2024-01-24 14:23:31,970] [INFO] DFAST_QC completed!
[2024-01-24 14:23:31,970] [INFO] Total running time: 0h0m59s