[2023-06-28 09:29:20,108] [INFO] DFAST_QC pipeline started.
[2023-06-28 09:29:20,109] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 09:29:20,109] [INFO] DQC Reference Directory: /var/lib/cwl/stgb86e0eb9-a0d7-43b3-9b8f-f581b44004f1/dqc_reference
[2023-06-28 09:29:21,340] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 09:29:21,341] [INFO] Task started: Prodigal
[2023-06-28 09:29:21,341] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7123c42-b4d8-4801-b9e5-4a1e22511129/GCA_019310195.1_ASM1931019v1_genomic.fna.gz | prodigal -d GCA_019310195.1_ASM1931019v1_genomic.fna/cds.fna -a GCA_019310195.1_ASM1931019v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 09:29:29,986] [INFO] Task succeeded: Prodigal
[2023-06-28 09:29:29,987] [INFO] Task started: HMMsearch
[2023-06-28 09:29:29,987] [INFO] Running command: hmmsearch --tblout GCA_019310195.1_ASM1931019v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb86e0eb9-a0d7-43b3-9b8f-f581b44004f1/dqc_reference/reference_markers.hmm GCA_019310195.1_ASM1931019v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 09:29:30,189] [INFO] Task succeeded: HMMsearch
[2023-06-28 09:29:30,190] [INFO] Found 6/6 markers.
[2023-06-28 09:29:30,222] [INFO] Query marker FASTA was written to GCA_019310195.1_ASM1931019v1_genomic.fna/markers.fasta
[2023-06-28 09:29:30,223] [INFO] Task started: Blastn
[2023-06-28 09:29:30,223] [INFO] Running command: blastn -query GCA_019310195.1_ASM1931019v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb86e0eb9-a0d7-43b3-9b8f-f581b44004f1/dqc_reference/reference_markers.fasta -out GCA_019310195.1_ASM1931019v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 09:29:30,910] [INFO] Task succeeded: Blastn
[2023-06-28 09:29:30,926] [INFO] Selected 27 target genomes.
[2023-06-28 09:29:30,927] [INFO] Target genome list was writen to GCA_019310195.1_ASM1931019v1_genomic.fna/target_genomes.txt
[2023-06-28 09:29:30,944] [INFO] Task started: fastANI
[2023-06-28 09:29:30,945] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7123c42-b4d8-4801-b9e5-4a1e22511129/GCA_019310195.1_ASM1931019v1_genomic.fna.gz --refList GCA_019310195.1_ASM1931019v1_genomic.fna/target_genomes.txt --output GCA_019310195.1_ASM1931019v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 09:29:51,617] [INFO] Task succeeded: fastANI
[2023-06-28 09:29:51,617] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb86e0eb9-a0d7-43b3-9b8f-f581b44004f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 09:29:51,617] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb86e0eb9-a0d7-43b3-9b8f-f581b44004f1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 09:29:51,636] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 09:29:51,637] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 09:29:51,637] [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
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	75.4353	115	1018	95	below_threshold
Thiohalorhabdus denitrificans	strain=HL 19	GCA_900101365.1	381306	381306	type	True	75.4116	58	1018	95	below_threshold
Thiohalorhabdus denitrificans	strain=HL 19	GCA_001399755.1	381306	381306	type	True	75.3675	61	1018	95	below_threshold
Deferrisoma camini	strain=S3R1	GCA_000526155.1	1035120	1035120	type	True	75.1561	100	1018	95	below_threshold
Xanthobacter autotrophicus	strain=DSM 432	GCA_005871085.1	280	280	type	True	75.1236	69	1018	95	below_threshold
Myxococcus xanthus	strain=DSM 16526	GCA_900106535.1	34	34	type	True	75.1161	109	1018	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	75.0679	90	1018	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.0594	164	1018	95	below_threshold
Myxococcus fulvus	strain=DSM 16525	GCA_900111765.1	33	33	type	True	75.0199	161	1018	95	below_threshold
Myxococcus virescens	strain=NBRC 100334	GCA_007989405.1	83456	83456	type	True	75.0099	124	1018	95	below_threshold
Thiohalocapsa halophila	strain=DSM 6210	GCA_016583825.1	69359	69359	type	True	75.0042	81	1018	95	below_threshold
Myxococcus virescens	strain=DSM 2260	GCA_900101905.1	83456	83456	type	True	75.0016	126	1018	95	below_threshold
Ornithinimicrobium cerasi	strain=CPCC 203383	GCA_003702705.1	2248773	2248773	type	True	74.9944	63	1018	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000273405.1	1063	1063	type	True	74.9359	61	1018	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_003324715.1	1063	1063	type	True	74.9359	61	1018	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000012905.2	1063	1063	type	True	74.9359	61	1018	95	below_threshold
Cereibacter sphaeroides	strain=2.4.1	GCA_000269625.2	1063	1063	type	True	74.9359	61	1018	95	below_threshold
Modestobacter caceresii	strain=KNN 45-2b	GCA_000761485.1	1522368	1522368	type	True	74.9222	92	1018	95	below_threshold
Myxococcus vastator	strain=AM301	GCA_010894475.1	2709664	2709664	type	True	74.9162	124	1018	95	below_threshold
Alsobacter soli	strain=SH9	GCA_003004785.1	2109933	2109933	type	True	74.8945	82	1018	95	below_threshold
Cereibacter sphaeroides	strain=NBRC 12203	GCA_007991035.1	1063	1063	type	True	74.8688	60	1018	95	below_threshold
Pleomorphomonas carboxyditropha	strain=SVCO-16	GCA_002770725.1	2023338	2023338	type	True	74.7938	78	1018	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	74.789	85	1018	95	below_threshold
Fodinicola acaciae	strain=GKU 173	GCA_010993745.1	2681555	2681555	type	True	74.7594	86	1018	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 09:29:51,639] [INFO] DFAST Taxonomy check result was written to GCA_019310195.1_ASM1931019v1_genomic.fna/tc_result.tsv
[2023-06-28 09:29:51,639] [INFO] ===== Taxonomy check completed =====
[2023-06-28 09:29:51,639] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 09:29:51,639] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb86e0eb9-a0d7-43b3-9b8f-f581b44004f1/dqc_reference/checkm_data
[2023-06-28 09:29:51,640] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 09:29:51,677] [INFO] Task started: CheckM
[2023-06-28 09:29:51,678] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019310195.1_ASM1931019v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019310195.1_ASM1931019v1_genomic.fna/checkm_input GCA_019310195.1_ASM1931019v1_genomic.fna/checkm_result
[2023-06-28 09:30:20,438] [INFO] Task succeeded: CheckM
[2023-06-28 09:30:20,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 09:30:20,455] [INFO] ===== Completeness check finished =====
[2023-06-28 09:30:20,456] [INFO] ===== Start GTDB Search =====
[2023-06-28 09:30:20,456] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019310195.1_ASM1931019v1_genomic.fna/markers.fasta)
[2023-06-28 09:30:20,456] [INFO] Task started: Blastn
[2023-06-28 09:30:20,456] [INFO] Running command: blastn -query GCA_019310195.1_ASM1931019v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb86e0eb9-a0d7-43b3-9b8f-f581b44004f1/dqc_reference/reference_markers_gtdb.fasta -out GCA_019310195.1_ASM1931019v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 09:30:21,579] [INFO] Task succeeded: Blastn
[2023-06-28 09:30:21,582] [INFO] Selected 21 target genomes.
[2023-06-28 09:30:21,583] [INFO] Target genome list was writen to GCA_019310195.1_ASM1931019v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 09:30:21,619] [INFO] Task started: fastANI
[2023-06-28 09:30:21,619] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7123c42-b4d8-4801-b9e5-4a1e22511129/GCA_019310195.1_ASM1931019v1_genomic.fna.gz --refList GCA_019310195.1_ASM1931019v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019310195.1_ASM1931019v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 09:30:35,913] [INFO] Task succeeded: fastANI
[2023-06-28 09:30:35,927] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 09:30:35,928] [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_002687015.1	s__GCA-2687015 sp002687015	77.0451	235	1018	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__GCA-2687015	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003576805.1	s__PR03 sp003576805	76.8794	280	1018	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905339255.1	s__MYXO sp905339255	76.6701	125	1018	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA9160;g__MYXO	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696485.1	s__CAADGG01 sp900696485	76.615	198	1018	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__CAADGG01	95.0	99.84	99.84	0.91	0.91	2	-
GCA_013215615.1	s__JABSQX01 sp013215615	76.5875	157	1018	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011055735.1	s__DSOP01 sp011055735	76.5512	256	1018	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__DSOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729515.1	s__GCA-2729515 sp002729515	76.3462	153	1018	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__GCA-2729515	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018262315.1	s__PR03 sp018262315	76.3245	164	1018	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__PR03;g__PR03	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215605.1	s__JABSQW01 sp013215605	76.1456	147	1018	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__SMWR01;g__JABSQW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713665.1	s__JADJOR01 sp016713665	75.8872	183	1018	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA4427;g__JADJOR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003751635.1	s__Inmirania thermothiophila	75.4523	113	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-100275;f__DSM-100275;g__Inmirania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964525.1	s__Anaeromyxobacter sp000964525	75.1563	140	1018	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013385.1	s__Anaeromyxobacter dehalogenans_B	75.1029	173	1018	d__Bacteria;p__Myxococcota;c__Myxococcia;o__Myxococcales;f__Anaeromyxobacteraceae;g__Anaeromyxobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000017645.1	s__Xanthobacter autotrophicus	75.0861	89	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Xanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487895.1	s__S144-34 sp015487895	75.052	52	1018	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S144-34;f__S144-34;g__S144-34	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908425.1	s__JAAAPF01 sp009908425	74.9926	69	1018	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Geminicoccales;f__Geminicoccaceae;g__JAAAPF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135735.1	s__Sorangium cellulosum_F	74.8176	176	1018	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__Polyangiaceae;g__Sorangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015390235.1	s__Quadrisphaera sp015390235	74.8121	100	1018	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Quadrisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 09:30:35,929] [INFO] GTDB search result was written to GCA_019310195.1_ASM1931019v1_genomic.fna/result_gtdb.tsv
[2023-06-28 09:30:35,930] [INFO] ===== GTDB Search completed =====
[2023-06-28 09:30:35,934] [INFO] DFAST_QC result json was written to GCA_019310195.1_ASM1931019v1_genomic.fna/dqc_result.json
[2023-06-28 09:30:35,935] [INFO] DFAST_QC completed!
[2023-06-28 09:30:35,935] [INFO] Total running time: 0h1m16s