[2024-01-24 11:05:27,656] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:27,659] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:27,660] [INFO] DQC Reference Directory: /var/lib/cwl/stgc834f416-3395-461f-b8a5-fef118700792/dqc_reference
[2024-01-24 11:05:29,121] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:29,122] [INFO] Task started: Prodigal
[2024-01-24 11:05:29,122] [INFO] Running command: gunzip -c /var/lib/cwl/stg58fed68a-2bec-4a18-b453-734b1ceaf721/GCF_016056295.1_ASM1605629v1_genomic.fna.gz | prodigal -d GCF_016056295.1_ASM1605629v1_genomic.fna/cds.fna -a GCF_016056295.1_ASM1605629v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:42,550] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:42,550] [INFO] Task started: HMMsearch
[2024-01-24 11:05:42,550] [INFO] Running command: hmmsearch --tblout GCF_016056295.1_ASM1605629v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc834f416-3395-461f-b8a5-fef118700792/dqc_reference/reference_markers.hmm GCF_016056295.1_ASM1605629v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:42,997] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:42,999] [INFO] Found 6/6 markers.
[2024-01-24 11:05:43,063] [INFO] Query marker FASTA was written to GCF_016056295.1_ASM1605629v1_genomic.fna/markers.fasta
[2024-01-24 11:05:43,064] [INFO] Task started: Blastn
[2024-01-24 11:05:43,064] [INFO] Running command: blastn -query GCF_016056295.1_ASM1605629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc834f416-3395-461f-b8a5-fef118700792/dqc_reference/reference_markers.fasta -out GCF_016056295.1_ASM1605629v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:43,721] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:43,726] [INFO] Selected 16 target genomes.
[2024-01-24 11:05:43,727] [INFO] Target genome list was writen to GCF_016056295.1_ASM1605629v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:43,734] [INFO] Task started: fastANI
[2024-01-24 11:05:43,734] [INFO] Running command: fastANI --query /var/lib/cwl/stg58fed68a-2bec-4a18-b453-734b1ceaf721/GCF_016056295.1_ASM1605629v1_genomic.fna.gz --refList GCF_016056295.1_ASM1605629v1_genomic.fna/target_genomes.txt --output GCF_016056295.1_ASM1605629v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:06,067] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:06,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc834f416-3395-461f-b8a5-fef118700792/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:06,068] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc834f416-3395-461f-b8a5-fef118700792/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:06,080] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:06:06,080] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:06:06,080] [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
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	80.4799	1180	2116	95	below_threshold
Nostoc punctiforme	strain=ATCC 29133; PCC 73102	GCA_000020025.1	272131	272131	type	True	80.046	1171	2116	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	78.3861	691	2116	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	78.2949	702	2116	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	77.6254	629	2116	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	77.624	630	2116	95	below_threshold
Brasilonema bromeliae	strain=SPC951	GCA_012912135.1	383615	383615	type	True	77.6196	496	2116	95	below_threshold
Fischerella muscicola	strain=PCC 7414	GCA_000317205.1	92938	92938	type	True	77.6064	591	2116	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	77.5686	533	2116	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	77.4003	566	2116	95	below_threshold
Aetokthonos hydrillicola	strain=CCALA 1050	GCA_017591665.1	1550245	1550245	type	True	77.0505	432	2116	95	below_threshold
Cylindrospermopsis raciborskii	strain=Cr2010	GCA_003367075.2	77022	77022	reftype	True	76.6396	144	2116	95	below_threshold
Argonema antarcticum	strain=A004/B2	GCA_023333585.1	2942763	2942763	type	True	75.8411	146	2116	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:06,087] [INFO] DFAST Taxonomy check result was written to GCF_016056295.1_ASM1605629v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:06,087] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:06,088] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:06,088] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc834f416-3395-461f-b8a5-fef118700792/dqc_reference/checkm_data
[2024-01-24 11:06:06,089] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:06,175] [INFO] Task started: CheckM
[2024-01-24 11:06:06,175] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016056295.1_ASM1605629v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016056295.1_ASM1605629v1_genomic.fna/checkm_input GCF_016056295.1_ASM1605629v1_genomic.fna/checkm_result
[2024-01-24 11:06:48,215] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:48,217] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:48,238] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:48,239] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:48,239] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016056295.1_ASM1605629v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:48,239] [INFO] Task started: Blastn
[2024-01-24 11:06:48,240] [INFO] Running command: blastn -query GCF_016056295.1_ASM1605629v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc834f416-3395-461f-b8a5-fef118700792/dqc_reference/reference_markers_gtdb.fasta -out GCF_016056295.1_ASM1605629v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:49,104] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:49,108] [INFO] Selected 21 target genomes.
[2024-01-24 11:06:49,109] [INFO] Target genome list was writen to GCF_016056295.1_ASM1605629v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:49,125] [INFO] Task started: fastANI
[2024-01-24 11:06:49,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg58fed68a-2bec-4a18-b453-734b1ceaf721/GCF_016056295.1_ASM1605629v1_genomic.fna.gz --refList GCF_016056295.1_ASM1605629v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016056295.1_ASM1605629v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:25,502] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:25,532] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:25,532] [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_016056295.1	s__Atlanticothrix silvestris	100.0	2106	2116	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Atlanticothrix	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003326215.1	s__Dendronalium minutum	81.6463	1400	2116	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dendronalium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017164015.1	s__Amazonocrinis sp017164015	81.1714	1327	2116	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Amazonocrinis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368335.1	s__Amazonocrinis sp002368335	81.1115	1292	2116	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Amazonocrinis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016056305.1	s__Amazonocrinis nigriterrae	81.0115	1285	2116	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Amazonocrinis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016056275.1	s__Dendronalium phyllosphericum	80.9762	1284	2116	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dendronalium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010091925.1	s__Nostoc sp010091925	80.74	1259	2116	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015207155.1	s__Nodularia sp015207155	80.7157	1183	2116	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nodularia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904695.1	s__Nostoc sp014904695	80.7061	1265	2116	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015206995.1	s__Nostoc sp015206995	80.6717	1077	2116	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698505.1	s__Nostoc foliaceum_A	80.6426	1250	2116	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	98.20	96.44	0.93	0.87	3	-
GCF_001712795.1	s__Nostoc sp001712795	80.4936	1178	2116	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014023275.1	s__Nostoc edaphicum_A	80.4095	1203	2116	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017115025.1	s__Nostoc sp017115025	80.281	1105	2116	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015206895.1	s__Nostoc sp015206895	80.211	1142	2116	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002246015.1	s__Nostoc sp002246015	80.1719	1179	2116	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017115165.1	s__Nostoc sp017115165	80.1234	1140	2116	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002949795.1	s__Nostoc sp002949795	80.0814	1105	2116	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020025.1	s__Nostoc punctiforme	80.0518	1169	2116	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017115045.1	s__Nostoc sp017115045	79.9761	1086	2116	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017115095.1	s__Nostoc sp017115095	79.944	1017	2116	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:25,534] [INFO] GTDB search result was written to GCF_016056295.1_ASM1605629v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:25,535] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:25,538] [INFO] DFAST_QC result json was written to GCF_016056295.1_ASM1605629v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:25,539] [INFO] DFAST_QC completed!
[2024-01-24 11:07:25,539] [INFO] Total running time: 0h1m58s