[2024-01-25 20:13:20,731] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:20,732] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:20,732] [INFO] DQC Reference Directory: /var/lib/cwl/stg76abe8c3-cc1a-4ea3-8a47-2bb17c50137e/dqc_reference
[2024-01-25 20:13:21,862] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:21,863] [INFO] Task started: Prodigal
[2024-01-25 20:13:21,863] [INFO] Running command: gunzip -c /var/lib/cwl/stgbad84bf5-dca9-4324-aa76-8e9f77739895/GCF_026240635.1_ASM2624063v1_genomic.fna.gz | prodigal -d GCF_026240635.1_ASM2624063v1_genomic.fna/cds.fna -a GCF_026240635.1_ASM2624063v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:32,192] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:32,192] [INFO] Task started: HMMsearch
[2024-01-25 20:13:32,192] [INFO] Running command: hmmsearch --tblout GCF_026240635.1_ASM2624063v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76abe8c3-cc1a-4ea3-8a47-2bb17c50137e/dqc_reference/reference_markers.hmm GCF_026240635.1_ASM2624063v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:32,423] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:32,424] [INFO] Found 6/6 markers.
[2024-01-25 20:13:32,456] [INFO] Query marker FASTA was written to GCF_026240635.1_ASM2624063v1_genomic.fna/markers.fasta
[2024-01-25 20:13:32,456] [INFO] Task started: Blastn
[2024-01-25 20:13:32,456] [INFO] Running command: blastn -query GCF_026240635.1_ASM2624063v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76abe8c3-cc1a-4ea3-8a47-2bb17c50137e/dqc_reference/reference_markers.fasta -out GCF_026240635.1_ASM2624063v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:32,987] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:32,989] [INFO] Selected 25 target genomes.
[2024-01-25 20:13:32,990] [INFO] Target genome list was writen to GCF_026240635.1_ASM2624063v1_genomic.fna/target_genomes.txt
[2024-01-25 20:13:33,016] [INFO] Task started: fastANI
[2024-01-25 20:13:33,016] [INFO] Running command: fastANI --query /var/lib/cwl/stgbad84bf5-dca9-4324-aa76-8e9f77739895/GCF_026240635.1_ASM2624063v1_genomic.fna.gz --refList GCF_026240635.1_ASM2624063v1_genomic.fna/target_genomes.txt --output GCF_026240635.1_ASM2624063v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:13:52,787] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:52,787] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76abe8c3-cc1a-4ea3-8a47-2bb17c50137e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:13:52,788] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76abe8c3-cc1a-4ea3-8a47-2bb17c50137e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:13:52,794] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:13:52,794] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:13:52,794] [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
Leptodesmis sichuanensis	strain=PKUAC-SCTA121	GCA_021379005.1	2906798	2906798	type	True	77.3963	124	1478	95	below_threshold
Thermoleptolyngbya sichuanensis	strain=PKUAC-SCTA183	GCA_013177315.1	2885951	2885951	type	True	76.7432	82	1478	95	below_threshold
Halomicronema hongdechloris	strain=C2206	GCA_002075285.3	1209493	1209493	type	True	76.3725	53	1478	95	below_threshold
Kovacikia minuta	strain=CCNU0001	GCA_020091585.1	2931930	2931930	type	True	75.999	84	1478	95	below_threshold
Spirulina major	strain=PCC 6313	GCA_001890765.1	270636	270636	type	True	75.9407	83	1478	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:13:52,796] [INFO] DFAST Taxonomy check result was written to GCF_026240635.1_ASM2624063v1_genomic.fna/tc_result.tsv
[2024-01-25 20:13:52,796] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:13:52,796] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:13:52,796] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76abe8c3-cc1a-4ea3-8a47-2bb17c50137e/dqc_reference/checkm_data
[2024-01-25 20:13:52,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:13:52,845] [INFO] Task started: CheckM
[2024-01-25 20:13:52,845] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026240635.1_ASM2624063v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026240635.1_ASM2624063v1_genomic.fna/checkm_input GCF_026240635.1_ASM2624063v1_genomic.fna/checkm_result
[2024-01-25 20:14:26,045] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:26,046] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:26,066] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:26,066] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:26,067] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026240635.1_ASM2624063v1_genomic.fna/markers.fasta)
[2024-01-25 20:14:26,067] [INFO] Task started: Blastn
[2024-01-25 20:14:26,067] [INFO] Running command: blastn -query GCF_026240635.1_ASM2624063v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76abe8c3-cc1a-4ea3-8a47-2bb17c50137e/dqc_reference/reference_markers_gtdb.fasta -out GCF_026240635.1_ASM2624063v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:26,785] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:26,789] [INFO] Selected 34 target genomes.
[2024-01-25 20:14:26,789] [INFO] Target genome list was writen to GCF_026240635.1_ASM2624063v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:26,819] [INFO] Task started: fastANI
[2024-01-25 20:14:26,819] [INFO] Running command: fastANI --query /var/lib/cwl/stgbad84bf5-dca9-4324-aa76-8e9f77739895/GCF_026240635.1_ASM2624063v1_genomic.fna.gz --refList GCF_026240635.1_ASM2624063v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026240635.1_ASM2624063v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:55,779] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:55,791] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:14:55,792] [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_013177315.1	s__O-77 sp013177315	77.0023	85	1478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__O-77	95.0	97.76	95.83	0.96	0.94	3	-
GCF_016403105.1	s__Nodosilinea sp016403105	76.7537	91	1478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000505665.1	s__Thermosynechococcus sp000505665	76.5992	54	1478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Thermosynechococcales;f__Thermosynechococcaceae;g__Thermosynechococcus	95.0	99.74	99.69	1.00	0.99	4	-
GCF_000317045.1	s__PCC-7407 sp000317045	76.4948	77	1478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__PCC-7407;f__PCC-7407;g__PCC-7407	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009939295.1	s__WVIC01 sp009939295	76.2419	71	1478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Thermosynechococcales;f__Thermosynechococcaceae;g__WVIC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014697375.1	s__Nodosilinea sp014697375	76.1511	84	1478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014697025.1	s__MUGG01 sp014697025	76.1322	82	1478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__MUGG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000733415.1	s__Elainella sp000733415	76.1166	83	1478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__Elainella	95.0	96.63	96.48	0.89	0.88	3	-
GCA_016743235.1	s__Pantanalinema sp016743235	76.0603	67	1478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__Pantanalinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332335.1	s__PCC-10802 sp000332335	76.0523	77	1478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae_A;g__PCC-10802	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012034055.1	s__JAAUSG01 sp012034055	75.8421	63	1478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__JAAUSG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000763385.1	s__Nodosilinea sp000763385	75.8049	79	1478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015272515.1	s__JSC-12 sp015272515	75.7928	59	1478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__JSC-12	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004292515.1	s__CACIAM-69d sp004292515	75.7584	62	1478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__CACIAM-69d;f__CACIAM-69d;g__CACIAM-69d	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014695325.1	s__Leptolyngbya_A sp014695325	75.7258	64	1478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__Leptolyngbya_A	95.0	99.45	99.45	0.94	0.94	2	-
GCA_003695655.1	s__O-77 sp003695655	75.7162	63	1478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__O-77	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012033355.1	s__JAAUTN01 sp012033355	75.4771	54	1478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__JAAUTN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014380065.1	s__Stenomitos sp014380065	75.3325	50	1478	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__Stenomitos	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:14:55,793] [INFO] GTDB search result was written to GCF_026240635.1_ASM2624063v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:55,794] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:55,796] [INFO] DFAST_QC result json was written to GCF_026240635.1_ASM2624063v1_genomic.fna/dqc_result.json
[2024-01-25 20:14:55,797] [INFO] DFAST_QC completed!
[2024-01-25 20:14:55,797] [INFO] Total running time: 0h1m35s