[2024-01-24 11:44:23,743] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,745] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,745] [INFO] DQC Reference Directory: /var/lib/cwl/stg14ca81b3-c85a-438a-b51d-3fa74e8a9cb9/dqc_reference
[2024-01-24 11:44:26,339] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,340] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,340] [INFO] Running command: gunzip -c /var/lib/cwl/stg505e732d-ec77-4d83-b8fd-2fbf26618c84/GCF_019891175.1_ASM1989117v1_genomic.fna.gz | prodigal -d GCF_019891175.1_ASM1989117v1_genomic.fna/cds.fna -a GCF_019891175.1_ASM1989117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:43,426] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:43,426] [INFO] Task started: HMMsearch
[2024-01-24 11:44:43,427] [INFO] Running command: hmmsearch --tblout GCF_019891175.1_ASM1989117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14ca81b3-c85a-438a-b51d-3fa74e8a9cb9/dqc_reference/reference_markers.hmm GCF_019891175.1_ASM1989117v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:43,774] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:43,777] [INFO] Found 6/6 markers.
[2024-01-24 11:44:43,828] [INFO] Query marker FASTA was written to GCF_019891175.1_ASM1989117v1_genomic.fna/markers.fasta
[2024-01-24 11:44:43,829] [INFO] Task started: Blastn
[2024-01-24 11:44:43,829] [INFO] Running command: blastn -query GCF_019891175.1_ASM1989117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14ca81b3-c85a-438a-b51d-3fa74e8a9cb9/dqc_reference/reference_markers.fasta -out GCF_019891175.1_ASM1989117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:44,389] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:44,393] [INFO] Selected 19 target genomes.
[2024-01-24 11:44:44,393] [INFO] Target genome list was writen to GCF_019891175.1_ASM1989117v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:44,445] [INFO] Task started: fastANI
[2024-01-24 11:44:44,446] [INFO] Running command: fastANI --query /var/lib/cwl/stg505e732d-ec77-4d83-b8fd-2fbf26618c84/GCF_019891175.1_ASM1989117v1_genomic.fna.gz --refList GCF_019891175.1_ASM1989117v1_genomic.fna/target_genomes.txt --output GCF_019891175.1_ASM1989117v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:07,647] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:07,647] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14ca81b3-c85a-438a-b51d-3fa74e8a9cb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:07,648] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14ca81b3-c85a-438a-b51d-3fa74e8a9cb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:07,655] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:45:07,656] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:07,656] [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
Leptothermofonsia sichuanensis	strain=PKUAC-SCTE412	GCA_019891175.1	2917832	2917832	type	True	100.0	2141	2142	95	conclusive
Thermoleptolyngbya sichuanensis	strain=PKUAC-SCTA183	GCA_013177315.1	2885951	2885951	type	True	78.2543	129	2142	95	below_threshold
Leptodesmis sichuanensis	strain=PKUAC-SCTA121	GCA_021379005.1	2906798	2906798	type	True	78.2283	226	2142	95	below_threshold
Kovacikia minuta	strain=CCNU0001	GCA_020091585.1	2931930	2931930	type	True	76.7902	378	2142	95	below_threshold
Neosynechococcus sphagnicola	strain=CAUP A 1101	GCA_000775285.1	1501145	1501145	type	True	76.5089	103	2142	95	below_threshold
Leptolyngbya boryana	strain=PCC 6306	GCA_000353285.1	1184	1184	type	True	76.359	63	2142	95	below_threshold
Fischerella muscicola	strain=PCC 7414	GCA_000317205.1	92938	92938	type	True	76.104	62	2142	95	below_threshold
Nostoc favosum	strain=CHAB 5714	GCA_020829495.1	2907819	2907819	type	True	75.4865	50	2142	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:07,657] [INFO] DFAST Taxonomy check result was written to GCF_019891175.1_ASM1989117v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:07,658] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:07,658] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:07,658] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14ca81b3-c85a-438a-b51d-3fa74e8a9cb9/dqc_reference/checkm_data
[2024-01-24 11:45:07,659] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:07,724] [INFO] Task started: CheckM
[2024-01-24 11:45:07,724] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019891175.1_ASM1989117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019891175.1_ASM1989117v1_genomic.fna/checkm_input GCF_019891175.1_ASM1989117v1_genomic.fna/checkm_result
[2024-01-24 11:46:01,366] [INFO] Task succeeded: CheckM
[2024-01-24 11:46:01,368] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:46:01,394] [INFO] ===== Completeness check finished =====
[2024-01-24 11:46:01,394] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:46:01,395] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019891175.1_ASM1989117v1_genomic.fna/markers.fasta)
[2024-01-24 11:46:01,395] [INFO] Task started: Blastn
[2024-01-24 11:46:01,395] [INFO] Running command: blastn -query GCF_019891175.1_ASM1989117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14ca81b3-c85a-438a-b51d-3fa74e8a9cb9/dqc_reference/reference_markers_gtdb.fasta -out GCF_019891175.1_ASM1989117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:46:02,225] [INFO] Task succeeded: Blastn
[2024-01-24 11:46:02,230] [INFO] Selected 28 target genomes.
[2024-01-24 11:46:02,230] [INFO] Target genome list was writen to GCF_019891175.1_ASM1989117v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:46:02,255] [INFO] Task started: fastANI
[2024-01-24 11:46:02,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg505e732d-ec77-4d83-b8fd-2fbf26618c84/GCF_019891175.1_ASM1989117v1_genomic.fna.gz --refList GCF_019891175.1_ASM1989117v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019891175.1_ASM1989117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:30,053] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:30,077] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:46:30,077] [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_001548395.1	s__O-77 sp001548395	77.9041	156	2142	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__O-77	95.0	95.35	95.35	0.93	0.93	2	-
GCA_000309945.1	s__JSC-12 sp000309945	77.0934	185	2142	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__JSC-12	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000775285.1	s__Neosynechococcus sphagnicola	76.5698	100	2142	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Neosynechococcales;f__Neosynechococcaceae;g__Neosynechococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000353285.1	s__Leptolyngbya boryana	76.5219	63	2142	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__Leptolyngbya	95.0	99.54	97.95	0.96	0.83	10	-
GCA_016743235.1	s__Pantanalinema sp016743235	76.4045	177	2142	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__Pantanalinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000022045.1	s__Cyanothece sp000022045	76.317	90	2142	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Thermosynechococcales;f__Thermosynechococcaceae;g__Cyanothece	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011331465.1	s__DSRU01 sp011331465	76.1698	136	2142	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__DSRU01	95.0	99.99	99.99	0.98	0.98	2	-
GCA_015272515.1	s__JSC-12 sp015272515	76.1608	145	2142	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_003695655.1	s__O-77 sp003695655	76.1538	87	2142	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__O-77	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003003795.1	s__Stenomitos frigidus	76.1216	148	2142	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__Stenomitos	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012034055.1	s__JAAUSG01 sp012034055	76.1213	181	2142	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__JAAUSG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003249025.1	s__ULC077BIN1 sp003249025	75.998	124	2142	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__ULC077BIN1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014695975.1	s__Stenomitos sp014695975	75.9324	158	2142	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__Stenomitos	95.0	96.78	96.78	0.86	0.86	2	-
GCF_014695955.1	s__FACHB-36 sp014695955	75.9134	91	2142	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__FACHB-36	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014695715.1	s__FACHB-68 sp014695715	75.8967	68	2142	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae_A;g__FACHB-68	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317045.1	s__PCC-7407 sp000317045	75.8366	100	2142	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	-
GCF_014849525.1	s__FACHB-SPT15 sp014849525	75.794	67	2142	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Coleofasciculaceae;g__FACHB-SPT15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014380065.1	s__Stenomitos sp014380065	75.7915	136	2142	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__Stenomitos	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010091945.1	s__Myxacorys almedinensis	75.7173	86	2142	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__Myxacorys	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014696135.1	s__Nodosilinea sp014696135	75.7028	64	2142	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	95.07	95.07	0.90	0.90	2	-
GCF_016888135.1	s__RECH01 sp016888135	75.6458	81	2142	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__RECH01	95.0	96.61	96.61	0.91	0.91	3	-
GCF_001895925.1	s__Phormidesmis_A priestleyi_A	75.6009	71	2142	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__Phormidesmis_A	95.0	99.98	99.98	0.97	0.97	3	-
GCA_015207365.1	s__FACHB-8 sp015207365	75.5015	96	2142	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__FACHB-8	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:30,079] [INFO] GTDB search result was written to GCF_019891175.1_ASM1989117v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:30,080] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:30,083] [INFO] DFAST_QC result json was written to GCF_019891175.1_ASM1989117v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:30,083] [INFO] DFAST_QC completed!
[2024-01-24 11:46:30,084] [INFO] Total running time: 0h2m6s