[2024-01-25 19:57:20,774] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:57:20,775] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:57:20,776] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1d24ef8-7de0-48d4-aeef-d020946ac753/dqc_reference
[2024-01-25 19:57:21,915] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:57:21,916] [INFO] Task started: Prodigal
[2024-01-25 19:57:21,916] [INFO] Running command: gunzip -c /var/lib/cwl/stg79a0b762-60a1-4e11-a578-7fc8de393ee9/GCF_026337845.1_ASM2633784v1_genomic.fna.gz | prodigal -d GCF_026337845.1_ASM2633784v1_genomic.fna/cds.fna -a GCF_026337845.1_ASM2633784v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:58:00,146] [INFO] Task succeeded: Prodigal
[2024-01-25 19:58:00,147] [INFO] Task started: HMMsearch
[2024-01-25 19:58:00,147] [INFO] Running command: hmmsearch --tblout GCF_026337845.1_ASM2633784v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1d24ef8-7de0-48d4-aeef-d020946ac753/dqc_reference/reference_markers.hmm GCF_026337845.1_ASM2633784v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:58:00,559] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:58:00,560] [INFO] Found 6/6 markers.
[2024-01-25 19:58:00,644] [INFO] Query marker FASTA was written to GCF_026337845.1_ASM2633784v1_genomic.fna/markers.fasta
[2024-01-25 19:58:00,645] [INFO] Task started: Blastn
[2024-01-25 19:58:00,645] [INFO] Running command: blastn -query GCF_026337845.1_ASM2633784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1d24ef8-7de0-48d4-aeef-d020946ac753/dqc_reference/reference_markers.fasta -out GCF_026337845.1_ASM2633784v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:58:01,332] [INFO] Task succeeded: Blastn
[2024-01-25 19:58:01,338] [INFO] Selected 26 target genomes.
[2024-01-25 19:58:01,338] [INFO] Target genome list was writen to GCF_026337845.1_ASM2633784v1_genomic.fna/target_genomes.txt
[2024-01-25 19:58:01,364] [INFO] Task started: fastANI
[2024-01-25 19:58:01,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg79a0b762-60a1-4e11-a578-7fc8de393ee9/GCF_026337845.1_ASM2633784v1_genomic.fna.gz --refList GCF_026337845.1_ASM2633784v1_genomic.fna/target_genomes.txt --output GCF_026337845.1_ASM2633784v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:58:31,045] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:31,046] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1d24ef8-7de0-48d4-aeef-d020946ac753/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:58:31,046] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1d24ef8-7de0-48d4-aeef-d020946ac753/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:58:31,060] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:58:31,060] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:58:31,061] [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
Plesiocystis pacifica	strain=SIR-1	GCA_000170895.1	191768	191768	type	True	76.165	939	3896	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	76.1317	1034	3896	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	76.1282	1069	3896	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	75.3743	616	3896	95	below_threshold
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	75.2325	212	3896	95	below_threshold
Geomonas paludis	strain=Red736	GCA_014193585.1	2740185	2740185	type	True	75.184	122	3896	95	below_threshold
Anaeromyxobacter dehalogenans	strain=2CP-1	GCA_000022145.1	161493	161493	type	True	75.1643	396	3896	95	below_threshold
Pelagerythrobacter rhizovicinus	strain=AY-3R	GCA_004135625.1	2268576	2268576	type	True	75.1258	113	3896	95	below_threshold
Salinisphaera halophila	strain=YIM 95161	GCA_003732545.1	1304158	1304158	type	True	75.0749	177	3896	95	below_threshold
Lysobacter maris	strain=KCTC 42381	GCA_006546735.2	1605891	1605891	type	True	75.0664	174	3896	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	75.0443	234	3896	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	75.0422	446	3896	95	below_threshold
Geomonas anaerohicana	strain=Red421	GCA_016458305.1	2798583	2798583	type	True	75.0357	108	3896	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	75.0236	242	3896	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	75.0212	243	3896	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	74.9774	644	3896	95	below_threshold
Methylobrevis albus	strain=L22	GCA_015904235.1	2793297	2793297	type	True	74.9555	238	3896	95	below_threshold
Ideonella azotifigens	strain=DSM 21438	GCA_006519715.1	513160	513160	type	True	74.9549	140	3896	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	74.9032	301	3896	95	below_threshold
Rhodoplanes roseus	strain=DSM 5909	GCA_003258865.1	29409	29409	type	True	74.8991	281	3896	95	below_threshold
Allokutzneria albata	strain=NRRL B-24461	GCA_000720955.1	211114	211114	type	True	74.8557	364	3896	95	below_threshold
Sinirhodobacter ferrireducens	strain=CCTCC AB2012026	GCA_004022265.1	1215032	1215032	type	True	74.8333	171	3896	95	below_threshold
Actinomadura namibiensis	strain=DSM 44197	GCA_014138665.1	182080	182080	type	True	74.8039	455	3896	95	below_threshold
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	74.7955	176	3896	95	below_threshold
Streptomyces spectabilis	strain=KCTC9218	GCA_022698305.1	68270	68270	type	True	74.7631	413	3896	95	below_threshold
Streptomyces smaragdinus	strain=RB5	GCA_009604385.1	2585196	2585196	type	True	74.6768	317	3896	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:58:31,062] [INFO] DFAST Taxonomy check result was written to GCF_026337845.1_ASM2633784v1_genomic.fna/tc_result.tsv
[2024-01-25 19:58:31,063] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:58:31,063] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:58:31,063] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1d24ef8-7de0-48d4-aeef-d020946ac753/dqc_reference/checkm_data
[2024-01-25 19:58:31,064] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:58:31,165] [INFO] Task started: CheckM
[2024-01-25 19:58:31,165] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026337845.1_ASM2633784v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026337845.1_ASM2633784v1_genomic.fna/checkm_input GCF_026337845.1_ASM2633784v1_genomic.fna/checkm_result
[2024-01-25 20:03:58,887] [INFO] Task succeeded: CheckM
[2024-01-25 20:03:58,888] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:03:58,926] [INFO] ===== Completeness check finished =====
[2024-01-25 20:03:58,927] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:03:58,928] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026337845.1_ASM2633784v1_genomic.fna/markers.fasta)
[2024-01-25 20:03:58,928] [INFO] Task started: Blastn
[2024-01-25 20:03:58,928] [INFO] Running command: blastn -query GCF_026337845.1_ASM2633784v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1d24ef8-7de0-48d4-aeef-d020946ac753/dqc_reference/reference_markers_gtdb.fasta -out GCF_026337845.1_ASM2633784v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:04:00,131] [INFO] Task succeeded: Blastn
[2024-01-25 20:04:00,134] [INFO] Selected 14 target genomes.
[2024-01-25 20:04:00,134] [INFO] Target genome list was writen to GCF_026337845.1_ASM2633784v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:04:00,162] [INFO] Task started: fastANI
[2024-01-25 20:04:00,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg79a0b762-60a1-4e11-a578-7fc8de393ee9/GCF_026337845.1_ASM2633784v1_genomic.fna.gz --refList GCF_026337845.1_ASM2633784v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026337845.1_ASM2633784v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:04:24,934] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:24,943] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:04:24,943] [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_016709225.1	s__Ga0077550 sp016709225	77.0038	1128	3896	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	99.66	99.17	0.98	0.94	4	-
GCA_001464385.1	s__Ga0077550 sp001464385	76.7751	1105	3896	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812955.1	s__Nannocystis sp013812955	76.3676	618	3896	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000170895.1	s__Plesiocystis pacifica	76.1729	928	3896	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Plesiocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002994615.1	s__Enhygromyxa salina_A	76.1607	864	3896	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002343915.1	s__Nannocystis exedens	76.1511	1054	3896	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.98	99.98	1.00	1.00	2	-
GCF_002994635.1	s__Enhygromyxa salina_B	76.0987	867	3896	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714285.1	s__Nannocystis sp016714285	76.0926	884	3896	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.25	99.25	0.96	0.96	2	-
GCA_902826865.1	s__Ga0077550 sp902826865	76.0606	488	3896	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793465.1	s__Nannocystis sp016793465	76.0371	1004	3896	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000737335.2	s__Enhygromyxa salina_C	76.0326	771	3896	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Enhygromyxa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712315.1	s__JADJRG01 sp016712315	75.799	598	3896	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__JADJRG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017996395.1	s__JAAYUB01 sp017996395	74.7716	119	3896	d__Bacteria;p__Acidobacteriota;c__UBA6911;o__JAAYUB01;f__JAAYUB01;g__JAAYUB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:04:24,944] [INFO] GTDB search result was written to GCF_026337845.1_ASM2633784v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:04:24,945] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:04:24,948] [INFO] DFAST_QC result json was written to GCF_026337845.1_ASM2633784v1_genomic.fna/dqc_result.json
[2024-01-25 20:04:24,948] [INFO] DFAST_QC completed!
[2024-01-25 20:04:24,948] [INFO] Total running time: 0h7m4s