[2024-01-24 11:34:53,613] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:53,615] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:53,615] [INFO] DQC Reference Directory: /var/lib/cwl/stgfcfc89ea-a218-489e-8357-832d09ce877e/dqc_reference
[2024-01-24 11:34:55,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:55,647] [INFO] Task started: Prodigal
[2024-01-24 11:34:55,647] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe87f31f-6c3d-475c-81fc-32fe1ec3a569/GCF_024178385.1_ASM2417838v1_genomic.fna.gz | prodigal -d GCF_024178385.1_ASM2417838v1_genomic.fna/cds.fna -a GCF_024178385.1_ASM2417838v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:07,365] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:07,365] [INFO] Task started: HMMsearch
[2024-01-24 11:35:07,365] [INFO] Running command: hmmsearch --tblout GCF_024178385.1_ASM2417838v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfcfc89ea-a218-489e-8357-832d09ce877e/dqc_reference/reference_markers.hmm GCF_024178385.1_ASM2417838v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:07,766] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:07,767] [INFO] Found 6/6 markers.
[2024-01-24 11:35:07,818] [INFO] Query marker FASTA was written to GCF_024178385.1_ASM2417838v1_genomic.fna/markers.fasta
[2024-01-24 11:35:07,819] [INFO] Task started: Blastn
[2024-01-24 11:35:07,819] [INFO] Running command: blastn -query GCF_024178385.1_ASM2417838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcfc89ea-a218-489e-8357-832d09ce877e/dqc_reference/reference_markers.fasta -out GCF_024178385.1_ASM2417838v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:08,405] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:08,408] [INFO] Selected 26 target genomes.
[2024-01-24 11:35:08,409] [INFO] Target genome list was writen to GCF_024178385.1_ASM2417838v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:08,434] [INFO] Task started: fastANI
[2024-01-24 11:35:08,434] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe87f31f-6c3d-475c-81fc-32fe1ec3a569/GCF_024178385.1_ASM2417838v1_genomic.fna.gz --refList GCF_024178385.1_ASM2417838v1_genomic.fna/target_genomes.txt --output GCF_024178385.1_ASM2417838v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:34,172] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:34,173] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfcfc89ea-a218-489e-8357-832d09ce877e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:34,173] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfcfc89ea-a218-489e-8357-832d09ce877e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:34,185] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:34,185] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:34,185] [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
Argonema antarcticum	strain=A004/B2	GCA_023333585.1	2942763	2942763	type	True	76.1275	171	1810	95	below_threshold
Argonema galeatum	strain=A003/A1	GCA_023333595.1	2942762	2942762	type	True	76.0827	158	1810	95	below_threshold
Brasilonema sennae	strain=CENA114	GCA_006968745.1	1397703	1397703	type	True	75.9482	93	1810	95	below_threshold
Allocoleopsis franciscana	strain=PCC 7113	GCA_000317515.1	2886352	2886352	type	True	75.7718	200	1810	95	below_threshold
Anabaena cylindrica	strain=NIES-19	GCA_002367955.1	1165	1165	type	True	75.7638	103	1810	95	below_threshold
Gloeothece citriformis	strain=PCC 7424	GCA_000021825.1	2546356	2546356	type	True	75.7593	64	1810	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	75.7592	116	1810	95	below_threshold
Anabaena cylindrica	strain=PCC 7122	GCA_000317695.1	1165	1165	type	True	75.7564	103	1810	95	below_threshold
Dulcicalothrix desertica	strain=PCC 7102	GCA_007830875.1	32056	32056	type	True	75.7133	73	1810	95	below_threshold
Iningainema tapete	strain=BLCC-T55	GCA_014698965.1	2806730	2806730	type	True	75.6251	103	1810	95	below_threshold
Aliterella atlantica	strain=CENA595	GCA_000952155.1	1827278	1827278	type	True	75.4919	62	1810	95	below_threshold
Dulcicalothrix desertica	strain=PCC 7102	GCA_003991905.1	32056	32056	type	True	75.4396	66	1810	95	below_threshold
Calothrix elsteri	strain=CCALA 953	GCA_002289455.1	1247191	1247191	type	True	75.3618	74	1810	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:34,187] [INFO] DFAST Taxonomy check result was written to GCF_024178385.1_ASM2417838v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:34,188] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:34,188] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:34,188] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfcfc89ea-a218-489e-8357-832d09ce877e/dqc_reference/checkm_data
[2024-01-24 11:35:34,190] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:34,258] [INFO] Task started: CheckM
[2024-01-24 11:35:34,258] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024178385.1_ASM2417838v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024178385.1_ASM2417838v1_genomic.fna/checkm_input GCF_024178385.1_ASM2417838v1_genomic.fna/checkm_result
[2024-01-24 11:36:13,159] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:13,160] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:13,185] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:13,185] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:13,185] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024178385.1_ASM2417838v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:13,186] [INFO] Task started: Blastn
[2024-01-24 11:36:13,186] [INFO] Running command: blastn -query GCF_024178385.1_ASM2417838v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcfc89ea-a218-489e-8357-832d09ce877e/dqc_reference/reference_markers_gtdb.fasta -out GCF_024178385.1_ASM2417838v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:13,982] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:13,985] [INFO] Selected 22 target genomes.
[2024-01-24 11:36:13,986] [INFO] Target genome list was writen to GCF_024178385.1_ASM2417838v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:14,006] [INFO] Task started: fastANI
[2024-01-24 11:36:14,007] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe87f31f-6c3d-475c-81fc-32fe1ec3a569/GCF_024178385.1_ASM2417838v1_genomic.fna.gz --refList GCF_024178385.1_ASM2417838v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024178385.1_ASM2417838v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:41,041] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:41,061] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:36:41,062] [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_003511885.1	s__UBA11153 sp003511885	83.0499	1180	1810	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__UBA11153	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014695295.1	s__Microcoleus sp014695295	76.3733	88	1810	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Microcoleus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015207375.1	s__LEGE-07092 sp015207375	76.3023	252	1810	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__LEGE-07092	95.0	99.97	99.97	0.97	0.97	2	-
GCF_014695895.1	s__PCC7113 sp014695895	76.0713	165	1810	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__PCC7113	95.0	98.22	98.22	0.91	0.91	2	-
GCF_000331305.1	s__Calothrix sp000331305	76.0204	66	1810	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Calothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000155555.1	s__Coleofasciculus chthonoplastes	75.9975	258	1810	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__Coleofasciculus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015207155.1	s__Nodularia sp015207155	75.9724	84	1810	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nodularia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014695915.1	s__FACHB-40 sp014695915	75.9382	97	1810	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__FACHB-T130;g__FACHB-40	95.0	96.30	95.91	0.87	0.85	6	-
GCA_010692325.1	s__Moorea sp010692325	75.859	140	1810	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__Moorea	95.0	97.88	97.68	0.88	0.86	3	-
GCF_014697615.1	s__Nostoc_B sp014697615	75.8183	109	1810	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Nostoc_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317515.1	s__PCC7113 sp000317515	75.7781	199	1810	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__PCC7113	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900299285.1	s__Dolichospermum sp900299285	75.7772	61	1810	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016056305.1	s__Amazonocrinis nigriterrae	75.702	113	1810	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Amazonocrinis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010672925.1	s__SIO2C1 sp010672925	75.6948	225	1810	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__SIO2C1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317535.1	s__Cylindrospermum stagnale	75.6858	124	1810	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Cylindrospermum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005402965.1	s__Dolichospermum planctonicum	75.6366	74	1810	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	98.27	96.37	0.91	0.88	5	-
GCA_002110465.1	s__Rippkaea sp002110465	75.5818	52	1810	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcystaceae_A;g__Rippkaea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010692425.1	s__SIO3C6 sp010692425	75.5524	139	1810	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__SIO3C6	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002368335.1	s__Amazonocrinis sp002368335	75.5372	119	1810	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Amazonocrinis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426925.1	s__Dolichospermum circinale	75.437	81	1810	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Dolichospermum	95.0	95.89	95.31	0.82	0.78	3	-
GCA_010672785.1	s__RDXV01 sp010672785	75.3605	80	1810	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__RDXV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015207585.1	s__LEGE-06147 sp015207585	75.2756	66	1810	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Xenococcaceae;g__LEGE-06147	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:41,063] [INFO] GTDB search result was written to GCF_024178385.1_ASM2417838v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:41,064] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:41,068] [INFO] DFAST_QC result json was written to GCF_024178385.1_ASM2417838v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:41,068] [INFO] DFAST_QC completed!
[2024-01-24 11:36:41,069] [INFO] Total running time: 0h1m47s