[2024-01-24 12:39:35,322] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:35,325] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:35,325] [INFO] DQC Reference Directory: /var/lib/cwl/stg2bc79b40-e03e-4679-b99b-af605b8de082/dqc_reference
[2024-01-24 12:39:36,531] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:36,532] [INFO] Task started: Prodigal
[2024-01-24 12:39:36,532] [INFO] Running command: gunzip -c /var/lib/cwl/stge7a2e862-0a0a-43f3-ae7f-abe2ff19f028/GCF_021379005.1_ASM2137900v1_genomic.fna.gz | prodigal -d GCF_021379005.1_ASM2137900v1_genomic.fna/cds.fna -a GCF_021379005.1_ASM2137900v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:50,616] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:50,617] [INFO] Task started: HMMsearch
[2024-01-24 12:39:50,617] [INFO] Running command: hmmsearch --tblout GCF_021379005.1_ASM2137900v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2bc79b40-e03e-4679-b99b-af605b8de082/dqc_reference/reference_markers.hmm GCF_021379005.1_ASM2137900v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:50,931] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:50,932] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge7a2e862-0a0a-43f3-ae7f-abe2ff19f028/GCF_021379005.1_ASM2137900v1_genomic.fna.gz]
[2024-01-24 12:39:50,977] [INFO] Query marker FASTA was written to GCF_021379005.1_ASM2137900v1_genomic.fna/markers.fasta
[2024-01-24 12:39:50,977] [INFO] Task started: Blastn
[2024-01-24 12:39:50,978] [INFO] Running command: blastn -query GCF_021379005.1_ASM2137900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bc79b40-e03e-4679-b99b-af605b8de082/dqc_reference/reference_markers.fasta -out GCF_021379005.1_ASM2137900v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:51,548] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:51,552] [INFO] Selected 22 target genomes.
[2024-01-24 12:39:51,553] [INFO] Target genome list was writen to GCF_021379005.1_ASM2137900v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:51,564] [INFO] Task started: fastANI
[2024-01-24 12:39:51,564] [INFO] Running command: fastANI --query /var/lib/cwl/stge7a2e862-0a0a-43f3-ae7f-abe2ff19f028/GCF_021379005.1_ASM2137900v1_genomic.fna.gz --refList GCF_021379005.1_ASM2137900v1_genomic.fna/target_genomes.txt --output GCF_021379005.1_ASM2137900v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:13,345] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:13,345] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2bc79b40-e03e-4679-b99b-af605b8de082/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:13,346] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2bc79b40-e03e-4679-b99b-af605b8de082/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:13,354] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:40:13,354] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:40:13,354] [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
Leptodesmis sichuanensis	strain=PKUAC-SCTA121	GCA_021379005.1	2906798	2906798	type	True	100.0	1782	1782	95	conclusive
Leptothermofonsia sichuanensis	strain=PKUAC-SCTE412	GCA_019891175.1	2917832	2917832	type	True	78.4261	215	1782	95	below_threshold
Kovacikia minuta	strain=CCNU0001	GCA_020091585.1	2931930	2931930	type	True	76.6713	209	1782	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_000317285.1	1124	1124	type	True	75.922	59	1782	95	below_threshold
Leptolyngbya boryana	strain=PCC 6306	GCA_000353285.1	1184	1184	type	True	75.9081	82	1782	95	below_threshold
Chlorogloeopsis fritschii	strain=PCC 6912	GCA_003990575.1	1124	1124	type	True	75.7646	58	1782	95	below_threshold
Argonema galeatum	strain=A003/A1	GCA_023333595.1	2942762	2942762	type	True	75.57	56	1782	95	below_threshold
Argonema antarcticum	strain=A004/B2	GCA_023333585.1	2942763	2942763	type	True	75.485	62	1782	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:13,362] [INFO] DFAST Taxonomy check result was written to GCF_021379005.1_ASM2137900v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:13,363] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:13,363] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:13,364] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2bc79b40-e03e-4679-b99b-af605b8de082/dqc_reference/checkm_data
[2024-01-24 12:40:13,365] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:13,436] [INFO] Task started: CheckM
[2024-01-24 12:40:13,436] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021379005.1_ASM2137900v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021379005.1_ASM2137900v1_genomic.fna/checkm_input GCF_021379005.1_ASM2137900v1_genomic.fna/checkm_result
[2024-01-24 12:40:58,568] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:58,570] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:58,592] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:58,592] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:58,592] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021379005.1_ASM2137900v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:58,593] [INFO] Task started: Blastn
[2024-01-24 12:40:58,593] [INFO] Running command: blastn -query GCF_021379005.1_ASM2137900v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2bc79b40-e03e-4679-b99b-af605b8de082/dqc_reference/reference_markers_gtdb.fasta -out GCF_021379005.1_ASM2137900v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:59,341] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:59,345] [INFO] Selected 25 target genomes.
[2024-01-24 12:40:59,345] [INFO] Target genome list was writen to GCF_021379005.1_ASM2137900v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:59,364] [INFO] Task started: fastANI
[2024-01-24 12:40:59,365] [INFO] Running command: fastANI --query /var/lib/cwl/stge7a2e862-0a0a-43f3-ae7f-abe2ff19f028/GCF_021379005.1_ASM2137900v1_genomic.fna.gz --refList GCF_021379005.1_ASM2137900v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021379005.1_ASM2137900v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:21,974] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:22,001] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:41:22,002] [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_015272325.1	s__JACYLU01 sp015272325	77.6919	115	1782	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__JACYLU01	95.0	98.57	98.57	0.96	0.96	2	-
GCA_000309945.1	s__JSC-12 sp000309945	76.9438	238	1782	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_012295525.1	s__Oxynema aestuarii	76.7117	62	1782	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Oscillatoriaceae;g__Oxynema	95.0	97.71	95.88	0.95	0.91	3	-
GCF_002215035.1	s__Leptolyngbya_A ohadii	76.6665	147	1782	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__Leptolyngbya_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016807185.1	s__ULC077BIN1 sp016807185	76.5192	168	1782	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__ULC077BIN1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012034055.1	s__JAAUSG01 sp012034055	76.4639	221	1782	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__JAAUSG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016403105.1	s__Nodosilinea sp016403105	76.4359	84	1782	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Phormidesmiales;f__Phormidesmiaceae;g__Nodosilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016743235.1	s__Pantanalinema sp016743235	76.3885	188	1782	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__Pantanalinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013393945.1	s__Trichormus sp013393945	76.3749	52	1782	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Nostocaceae;g__Trichormus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015272515.1	s__JSC-12 sp015272515	76.3493	270	1782	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_012516315.1	s__Limnospira fusiformis	76.3402	52	1782	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__Limnospira	95.0	99.21	98.53	0.94	0.92	10	-
GCA_003249025.1	s__ULC077BIN1 sp003249025	76.1562	175	1782	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__ULC077BIN1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000733415.1	s__Elainella sp000733415	76.1207	117	1782	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__Elainella	95.0	96.63	96.48	0.89	0.88	3	-
GCA_012033335.1	s__JAAURB01 sp012033335	76.0622	63	1782	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Cyanobacteriales;f__Microcoleaceae;g__JAAURB01	95.0	99.92	99.92	0.98	0.98	2	-
GCF_014695955.1	s__FACHB-36 sp014695955	76.0344	75	1782	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__FACHB-36	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012032525.1	s__JAAUSV01 sp012032525	76.0289	78	1782	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__JAAUSV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014380065.1	s__Stenomitos sp014380065	75.8261	101	1782	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__Stenomitos	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014698235.1	s__CACIAM-69d sp001698445	75.7831	73	1782	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__CACIAM-69d;f__CACIAM-69d;g__CACIAM-69d	95.0	98.17	97.78	0.95	0.92	7	-
GCF_014695575.1	s__FACHB-8 sp014695575	75.7126	110	1782	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Elainellales;f__Elainellaceae;g__FACHB-8	95.0	99.92	99.92	0.94	0.94	2	-
GCA_012031975.1	s__JAAUSA01 sp012031975	75.2811	55	1782	d__Bacteria;p__Cyanobacteria;c__Cyanobacteriia;o__Leptolyngbyales;f__Leptolyngbyaceae;g__JAAUSA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:22,003] [INFO] GTDB search result was written to GCF_021379005.1_ASM2137900v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:22,005] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:22,009] [INFO] DFAST_QC result json was written to GCF_021379005.1_ASM2137900v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:22,009] [INFO] DFAST_QC completed!
[2024-01-24 12:41:22,009] [INFO] Total running time: 0h1m47s