[2023-06-05 02:54:12,642] [INFO] DFAST_QC pipeline started.
[2023-06-05 02:54:12,648] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 02:54:12,648] [INFO] DQC Reference Directory: /var/lib/cwl/stg34b66c51-403c-4787-9a51-0071e52aeb1a/dqc_reference
[2023-06-05 02:54:13,836] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 02:54:13,837] [INFO] Task started: Prodigal
[2023-06-05 02:54:13,837] [INFO] Running command: gunzip -c /var/lib/cwl/stgdc8dc1c5-c19b-4a9b-9ee6-122fba0a4b6a/GCA_010671925.1_ASM1067192v1_genomic.fna.gz | prodigal -d GCA_010671925.1_ASM1067192v1_genomic.fna/cds.fna -a GCA_010671925.1_ASM1067192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 02:54:35,768] [INFO] Task succeeded: Prodigal
[2023-06-05 02:54:35,768] [INFO] Task started: HMMsearch
[2023-06-05 02:54:35,768] [INFO] Running command: hmmsearch --tblout GCA_010671925.1_ASM1067192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34b66c51-403c-4787-9a51-0071e52aeb1a/dqc_reference/reference_markers.hmm GCA_010671925.1_ASM1067192v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 02:54:36,242] [INFO] Task succeeded: HMMsearch
[2023-06-05 02:54:36,243] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdc8dc1c5-c19b-4a9b-9ee6-122fba0a4b6a/GCA_010671925.1_ASM1067192v1_genomic.fna.gz]
[2023-06-05 02:54:36,313] [INFO] Query marker FASTA was written to GCA_010671925.1_ASM1067192v1_genomic.fna/markers.fasta
[2023-06-05 02:54:36,313] [INFO] Task started: Blastn
[2023-06-05 02:54:36,313] [INFO] Running command: blastn -query GCA_010671925.1_ASM1067192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34b66c51-403c-4787-9a51-0071e52aeb1a/dqc_reference/reference_markers.fasta -out GCA_010671925.1_ASM1067192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:54:36,869] [INFO] Task succeeded: Blastn
[2023-06-05 02:54:36,874] [INFO] Selected 15 target genomes.
[2023-06-05 02:54:36,875] [INFO] Target genome list was writen to GCA_010671925.1_ASM1067192v1_genomic.fna/target_genomes.txt
[2023-06-05 02:54:36,880] [INFO] Task started: fastANI
[2023-06-05 02:54:36,880] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc8dc1c5-c19b-4a9b-9ee6-122fba0a4b6a/GCA_010671925.1_ASM1067192v1_genomic.fna.gz --refList GCA_010671925.1_ASM1067192v1_genomic.fna/target_genomes.txt --output GCA_010671925.1_ASM1067192v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 02:55:29,086] [INFO] Task succeeded: fastANI
[2023-06-05 02:55:29,087] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34b66c51-403c-4787-9a51-0071e52aeb1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 02:55:29,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34b66c51-403c-4787-9a51-0071e52aeb1a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 02:55:29,103] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 02:55:29,103] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 02:55:29,103] [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
Moorena producens	strain=3L	GCA_001942475.1	1155739	1155739	type	True	93.2212	2367	3300	95	below_threshold
Moorena producens	strain=3L	GCA_000211815.1	1155739	1155739	type	True	93.1795	2338	3300	95	below_threshold
Allocoleopsis franciscana	strain=PCC 7113	GCA_000317515.1	2886352	2886352	type	True	76.1542	256	3300	95	below_threshold
Leptothermofonsia sichuanensis	strain=PKUAC-SCTE412	GCA_019891175.1	2917832	2917832	type	True	76.0083	58	3300	95	below_threshold
Kovacikia minuta	strain=CCNU0001	GCA_020091585.1	2931930	2931930	type	True	75.9069	78	3300	95	below_threshold
Oscillatoria acuminata	strain=PCC 6304	GCA_000317105.1	118323	118323	type	True	75.9039	87	3300	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	75.8548	98	3300	95	below_threshold
Crocosphaera subtropica	strain=ATCC 51142	GCA_000017845.1	2546360	2546360	type	True	75.8382	79	3300	95	below_threshold
Stanieria cyanosphaera	strain=PCC 7437	GCA_000317575.1	102116	102116	type	True	75.8079	84	3300	95	below_threshold
Crocosphaera chwakensis	strain=CCY0110	GCA_000169335.1	2546361	2546361	type	True	75.7981	73	3300	95	below_threshold
Crocosphaera watsonii	strain=WH 8501	GCA_000167195.1	263511	263511	suspected-type	True	75.7349	77	3300	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	75.5601	130	3300	95	below_threshold
Argonema antarcticum	strain=A004/B2	GCA_023333585.1	2942763	2942763	type	True	75.5386	113	3300	95	below_threshold
Argonema galeatum	strain=A003/A1	GCA_023333595.1	2942762	2942762	type	True	75.4798	124	3300	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 02:55:29,127] [INFO] DFAST Taxonomy check result was written to GCA_010671925.1_ASM1067192v1_genomic.fna/tc_result.tsv
[2023-06-05 02:55:29,134] [INFO] ===== Taxonomy check completed =====
[2023-06-05 02:55:29,135] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 02:55:29,135] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34b66c51-403c-4787-9a51-0071e52aeb1a/dqc_reference/checkm_data
[2023-06-05 02:55:29,136] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 02:55:29,225] [INFO] Task started: CheckM
[2023-06-05 02:55:29,225] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_010671925.1_ASM1067192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_010671925.1_ASM1067192v1_genomic.fna/checkm_input GCA_010671925.1_ASM1067192v1_genomic.fna/checkm_result
[2023-06-05 02:56:35,011] [INFO] Task succeeded: CheckM
[2023-06-05 02:56:35,012] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 02:56:35,038] [INFO] ===== Completeness check finished =====
[2023-06-05 02:56:35,038] [INFO] ===== Start GTDB Search =====
[2023-06-05 02:56:35,039] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_010671925.1_ASM1067192v1_genomic.fna/markers.fasta)
[2023-06-05 02:56:35,039] [INFO] Task started: Blastn
[2023-06-05 02:56:35,039] [INFO] Running command: blastn -query GCA_010671925.1_ASM1067192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34b66c51-403c-4787-9a51-0071e52aeb1a/dqc_reference/reference_markers_gtdb.fasta -out GCA_010671925.1_ASM1067192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 02:56:35,715] [INFO] Task succeeded: Blastn
[2023-06-05 02:56:35,719] [INFO] Selected 7 target genomes.
[2023-06-05 02:56:35,720] [INFO] Target genome list was writen to GCA_010671925.1_ASM1067192v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 02:56:35,728] [INFO] Task started: fastANI
[2023-06-05 02:56:35,728] [INFO] Running command: fastANI --query /var/lib/cwl/stgdc8dc1c5-c19b-4a9b-9ee6-122fba0a4b6a/GCA_010671925.1_ASM1067192v1_genomic.fna.gz --refList GCA_010671925.1_ASM1067192v1_genomic.fna/target_genomes_gtdb.txt --output GCA_010671925.1_ASM1067192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 02:58:50,021] [INFO] Task succeeded: fastANI
[2023-06-05 02:58:50,031] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 02:58:50,031] [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_010671925.1	s__Moorea sp010671925	100.0	3299	3300	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__Moorea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_010692325.1	s__Moorea sp010692325	94.034	2060	3300	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__Moorea	95.0	97.88	97.68	0.88	0.86	3	-
GCF_001767235.1	s__Moorea producens_A	93.4425	2618	3300	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__Moorea	95.0	96.04	96.04	0.84	0.84	2	-
GCF_001942495.1	s__Moorea bouillonii	93.2637	2328	3300	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__Moorea	95.0	96.52	96.51	0.86	0.86	3	-
GCF_000211815.1	s__Moorea producens	93.2012	2336	3300	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__Moorea	95.0	98.41	95.37	0.92	0.86	6	-
GCA_010692395.1	s__Moorea sp010692395	92.6076	2062	3300	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__Moorea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011524395.1	s__Moorea sp011524395	92.4165	2074	3300	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__Moorea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 02:58:50,033] [INFO] GTDB search result was written to GCA_010671925.1_ASM1067192v1_genomic.fna/result_gtdb.tsv
[2023-06-05 02:58:50,034] [INFO] ===== GTDB Search completed =====
[2023-06-05 02:58:50,037] [INFO] DFAST_QC result json was written to GCA_010671925.1_ASM1067192v1_genomic.fna/dqc_result.json
[2023-06-05 02:58:50,037] [INFO] DFAST_QC completed!
[2023-06-05 02:58:50,037] [INFO] Total running time: 0h4m37s