[2024-01-24 13:56:56,487] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:56,489] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:56,489] [INFO] DQC Reference Directory: /var/lib/cwl/stgf849a33c-f6ea-4e67-b644-ee8e5cdc0567/dqc_reference
[2024-01-24 13:56:57,717] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:57,718] [INFO] Task started: Prodigal
[2024-01-24 13:56:57,719] [INFO] Running command: gunzip -c /var/lib/cwl/stgb5c833e1-3da6-416b-a413-ec85013499b2/GCF_000952155.1_asmbly001_genomic.fna.gz | prodigal -d GCF_000952155.1_asmbly001_genomic.fna/cds.fna -a GCF_000952155.1_asmbly001_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:08,315] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:08,316] [INFO] Task started: HMMsearch
[2024-01-24 13:57:08,316] [INFO] Running command: hmmsearch --tblout GCF_000952155.1_asmbly001_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf849a33c-f6ea-4e67-b644-ee8e5cdc0567/dqc_reference/reference_markers.hmm GCF_000952155.1_asmbly001_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:08,676] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:08,678] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb5c833e1-3da6-416b-a413-ec85013499b2/GCF_000952155.1_asmbly001_genomic.fna.gz]
[2024-01-24 13:57:08,729] [INFO] Query marker FASTA was written to GCF_000952155.1_asmbly001_genomic.fna/markers.fasta
[2024-01-24 13:57:08,730] [INFO] Task started: Blastn
[2024-01-24 13:57:08,730] [INFO] Running command: blastn -query GCF_000952155.1_asmbly001_genomic.fna/markers.fasta -db /var/lib/cwl/stgf849a33c-f6ea-4e67-b644-ee8e5cdc0567/dqc_reference/reference_markers.fasta -out GCF_000952155.1_asmbly001_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:09,320] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:09,323] [INFO] Selected 18 target genomes.
[2024-01-24 13:57:09,324] [INFO] Target genome list was writen to GCF_000952155.1_asmbly001_genomic.fna/target_genomes.txt
[2024-01-24 13:57:09,332] [INFO] Task started: fastANI
[2024-01-24 13:57:09,333] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5c833e1-3da6-416b-a413-ec85013499b2/GCF_000952155.1_asmbly001_genomic.fna.gz --refList GCF_000952155.1_asmbly001_genomic.fna/target_genomes.txt --output GCF_000952155.1_asmbly001_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:25,478] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:25,479] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf849a33c-f6ea-4e67-b644-ee8e5cdc0567/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:25,480] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf849a33c-f6ea-4e67-b644-ee8e5cdc0567/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:25,495] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:25,495] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:25,496] [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
Aliterella atlantica	strain=CENA595	GCA_000952155.1	1827278	1827278	type	True	100.0	1720	1723	95	conclusive
Dulcicalothrix desertica	strain=PCC 7102	GCA_007830875.1	32056	32056	type	True	76.4052	90	1723	95	below_threshold
Gloeocapsopsis dulcis	strain=AAB1	GCA_002964865.1	2859516	2859516	type	True	76.2325	179	1723	95	below_threshold
Dulcicalothrix desertica	strain=PCC 7102	GCA_003991905.1	32056	32056	type	True	76.1232	91	1723	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	76.0716	165	1723	95	below_threshold
Fischerella thermalis	strain=PCC 7521	GCA_000317225.1	372787	372787	type	True	76.0	112	1723	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	75.9708	170	1723	95	below_threshold
Argonema galeatum	strain=A003/A1	GCA_023333595.1	2942762	2942762	type	True	75.8835	106	1723	95	below_threshold
Argonema antarcticum	strain=A004/B2	GCA_023333585.1	2942763	2942763	type	True	75.7781	123	1723	95	below_threshold
Okeania hirsuta	strain=PAB10Feb10-1	GCA_003838195.1	1458930	1458930	type	True	75.1552	61	1723	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:25,498] [INFO] DFAST Taxonomy check result was written to GCF_000952155.1_asmbly001_genomic.fna/tc_result.tsv
[2024-01-24 13:57:25,498] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:25,499] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:25,499] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf849a33c-f6ea-4e67-b644-ee8e5cdc0567/dqc_reference/checkm_data
[2024-01-24 13:57:25,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:25,557] [INFO] Task started: CheckM
[2024-01-24 13:57:25,557] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000952155.1_asmbly001_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000952155.1_asmbly001_genomic.fna/checkm_input GCF_000952155.1_asmbly001_genomic.fna/checkm_result
[2024-01-24 13:58:01,468] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:01,470] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:01,493] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:01,494] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:01,494] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000952155.1_asmbly001_genomic.fna/markers.fasta)
[2024-01-24 13:58:01,495] [INFO] Task started: Blastn
[2024-01-24 13:58:01,495] [INFO] Running command: blastn -query GCF_000952155.1_asmbly001_genomic.fna/markers.fasta -db /var/lib/cwl/stgf849a33c-f6ea-4e67-b644-ee8e5cdc0567/dqc_reference/reference_markers_gtdb.fasta -out GCF_000952155.1_asmbly001_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:02,280] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:02,284] [INFO] Selected 18 target genomes.
[2024-01-24 13:58:02,284] [INFO] Target genome list was writen to GCF_000952155.1_asmbly001_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:02,305] [INFO] Task started: fastANI
[2024-01-24 13:58:02,306] [INFO] Running command: fastANI --query /var/lib/cwl/stgb5c833e1-3da6-416b-a413-ec85013499b2/GCF_000952155.1_asmbly001_genomic.fna.gz --refList GCF_000952155.1_asmbly001_genomic.fna/target_genomes_gtdb.txt --output GCF_000952155.1_asmbly001_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:23,810] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:23,825] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:23,825] [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_000952155.1	s__Aliterella atlantica	100.0	1720	1723	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Chroococcidiopsidaceae;g__Aliterella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003003885.1	s__Aliterella sp003003885	78.5699	666	1723	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Chroococcidiopsidaceae;g__Aliterella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013698215.1	s__Aliterella sp013698215	78.4846	357	1723	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Chroococcidiopsidaceae;g__Aliterella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000332075.2	s__Aliterella sp000332075	78.3411	672	1723	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Chroococcidiopsidaceae;g__Aliterella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479905.1	s__Aliterella sp905479905	78.0866	394	1723	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Chroococcidiopsidaceae;g__Aliterella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014697075.1	s__Aulosira sp014697075	76.8553	182	1723	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Aulosira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003326205.1	s__Nostoc sp003326205	76.4504	169	1723	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698115.1	s__Nostoc sp014698115	76.3435	166	1723	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002964865.1	s__Gloeocapsopsis dulcis	76.2325	179	1723	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Chroococcidiopsidaceae;g__Gloeocapsopsis	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000317205.1	s__Fischerella muscicola	76.0765	138	1723	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	99.84	99.68	0.97	0.95	3	-
GCF_014697355.1	s__Nostoc calcicola	76.0659	170	1723	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	99.97	99.97	0.98	0.98	2	-
GCF_002218085.1	s__Hassallia sp002218085	76.0434	179	1723	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Hassallia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317225.1	s__Fischerella thermalis	76.0	112	1723	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Fischerella	95.0	98.97	96.56	0.93	0.78	35	-
GCF_014698505.1	s__Nostoc foliaceum_A	75.9273	154	1723	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc	95.0	98.20	96.44	0.93	0.87	3	-
GCF_002368195.1	s__Aulosira sp002368195	75.9071	185	1723	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Aulosira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014695585.1	s__FACHB-831 sp014695585	75.873	116	1723	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__FACHB-T130;g__FACHB-831	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000613065.1	s__Richelia intracellularis_B	75.82	64	1723	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Richelia	95.0	98.82	98.82	0.85	0.85	2	-
GCA_011332035.1	s__Trichormus sp011332035	75.7643	136	1723	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Trichormus	95.0	99.98	99.98	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:58:23,827] [INFO] GTDB search result was written to GCF_000952155.1_asmbly001_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:23,827] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:23,831] [INFO] DFAST_QC result json was written to GCF_000952155.1_asmbly001_genomic.fna/dqc_result.json
[2024-01-24 13:58:23,831] [INFO] DFAST_QC completed!
[2024-01-24 13:58:23,831] [INFO] Total running time: 0h1m27s