[2024-01-24 11:34:42,960] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:42,962] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:42,962] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c91e4c1-3f89-45c7-9e91-dbb27675870d/dqc_reference
[2024-01-24 11:34:44,360] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:44,361] [INFO] Task started: Prodigal
[2024-01-24 11:34:44,361] [INFO] Running command: gunzip -c /var/lib/cwl/stgea612de3-b80c-4bca-bec5-d84ad4083604/GCF_019195455.1_ASM1919545v2_genomic.fna.gz | prodigal -d GCF_019195455.1_ASM1919545v2_genomic.fna/cds.fna -a GCF_019195455.1_ASM1919545v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:34:59,776] [INFO] Task succeeded: Prodigal
[2024-01-24 11:34:59,777] [INFO] Task started: HMMsearch
[2024-01-24 11:34:59,777] [INFO] Running command: hmmsearch --tblout GCF_019195455.1_ASM1919545v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c91e4c1-3f89-45c7-9e91-dbb27675870d/dqc_reference/reference_markers.hmm GCF_019195455.1_ASM1919545v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:00,095] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:00,096] [INFO] Found 6/6 markers.
[2024-01-24 11:35:00,137] [INFO] Query marker FASTA was written to GCF_019195455.1_ASM1919545v2_genomic.fna/markers.fasta
[2024-01-24 11:35:00,137] [INFO] Task started: Blastn
[2024-01-24 11:35:00,137] [INFO] Running command: blastn -query GCF_019195455.1_ASM1919545v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c91e4c1-3f89-45c7-9e91-dbb27675870d/dqc_reference/reference_markers.fasta -out GCF_019195455.1_ASM1919545v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:01,051] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:01,055] [INFO] Selected 29 target genomes.
[2024-01-24 11:35:01,055] [INFO] Target genome list was writen to GCF_019195455.1_ASM1919545v2_genomic.fna/target_genomes.txt
[2024-01-24 11:35:01,063] [INFO] Task started: fastANI
[2024-01-24 11:35:01,063] [INFO] Running command: fastANI --query /var/lib/cwl/stgea612de3-b80c-4bca-bec5-d84ad4083604/GCF_019195455.1_ASM1919545v2_genomic.fna.gz --refList GCF_019195455.1_ASM1919545v2_genomic.fna/target_genomes.txt --output GCF_019195455.1_ASM1919545v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:23,462] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:23,462] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c91e4c1-3f89-45c7-9e91-dbb27675870d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:23,462] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c91e4c1-3f89-45c7-9e91-dbb27675870d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:23,487] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:23,487] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:23,487] [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
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	78.0396	494	1440	95	below_threshold
Rhodophyticola porphyridii	strain=MA-7-27	GCA_003688285.1	1852017	1852017	type	True	77.8121	387	1440	95	below_threshold
Nioella ostreopsis	strain=Z7-4	GCA_004000255.1	2448479	2448479	type	True	77.7961	420	1440	95	below_threshold
Roseovarius atlanticus	strain=R12B	GCA_001441615.1	1641875	1641875	type	True	77.7477	283	1440	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	77.7047	286	1440	95	below_threshold
Nioella nitratireducens	strain=SSW136	GCA_001879715.1	1287720	1287720	type	True	77.4903	360	1440	95	below_threshold
Lutimaribacter saemankumensis	strain=DSM 28010	GCA_900100005.1	490829	490829	type	True	77.3905	274	1440	95	below_threshold
Thalassorhabdomicrobium marinisediminis	strain=BH-SD16	GCA_003072065.1	2170577	2170577	type	True	77.3814	281	1440	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	77.3383	315	1440	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	77.3119	277	1440	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	77.311	288	1440	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	77.2908	293	1440	95	below_threshold
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	77.2755	295	1440	95	below_threshold
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	77.2344	249	1440	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	77.2156	309	1440	95	below_threshold
Pseudodonghicola xiamenensis	strain=CGMCC 1.7081	GCA_014653505.1	337702	337702	type	True	77.2059	256	1440	95	below_threshold
Loktanella atrilutea	strain=DSM 29326	GCA_900128995.1	366533	366533	type	True	77.1988	277	1440	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.1518	289	1440	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	77.1484	258	1440	95	below_threshold
Salipiger thiooxidans	strain=DSM 10146	GCA_900102075.1	282683	282683	type	True	77.1172	318	1440	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	77.0976	295	1440	95	below_threshold
Hasllibacter halocynthiae	strain=DSM 29318	GCA_003003095.1	595589	595589	type	True	77.0731	180	1440	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	77.0519	287	1440	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	77.0233	248	1440	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.0154	251	1440	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	77.0082	302	1440	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	76.8945	236	1440	95	below_threshold
Mangrovicoccus ximenensis	strain=T1lg56	GCA_003056725.1	1911570	1911570	type	True	76.8567	235	1440	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	76.8502	236	1440	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:23,489] [INFO] DFAST Taxonomy check result was written to GCF_019195455.1_ASM1919545v2_genomic.fna/tc_result.tsv
[2024-01-24 11:35:23,490] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:23,490] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:23,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c91e4c1-3f89-45c7-9e91-dbb27675870d/dqc_reference/checkm_data
[2024-01-24 11:35:23,492] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:23,536] [INFO] Task started: CheckM
[2024-01-24 11:35:23,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019195455.1_ASM1919545v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019195455.1_ASM1919545v2_genomic.fna/checkm_input GCF_019195455.1_ASM1919545v2_genomic.fna/checkm_result
[2024-01-24 11:36:10,395] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:10,397] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:10,412] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:10,412] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:10,413] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019195455.1_ASM1919545v2_genomic.fna/markers.fasta)
[2024-01-24 11:36:10,413] [INFO] Task started: Blastn
[2024-01-24 11:36:10,413] [INFO] Running command: blastn -query GCF_019195455.1_ASM1919545v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c91e4c1-3f89-45c7-9e91-dbb27675870d/dqc_reference/reference_markers_gtdb.fasta -out GCF_019195455.1_ASM1919545v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:12,126] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:12,130] [INFO] Selected 15 target genomes.
[2024-01-24 11:36:12,131] [INFO] Target genome list was writen to GCF_019195455.1_ASM1919545v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:12,150] [INFO] Task started: fastANI
[2024-01-24 11:36:12,150] [INFO] Running command: fastANI --query /var/lib/cwl/stgea612de3-b80c-4bca-bec5-d84ad4083604/GCF_019195455.1_ASM1919545v2_genomic.fna.gz --refList GCF_019195455.1_ASM1919545v2_genomic.fna/target_genomes_gtdb.txt --output GCF_019195455.1_ASM1919545v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:24,210] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:24,227] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:24,227] [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_019195455.1	s__Roseicyclus sp001650845	100.0	1440	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	96.25	96.25	0.88	0.88	2	conclusive
GCF_000013565.1	s__Roseicyclus sp000013565	81.2542	930	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689645.1	s__Roseicyclus sp015689645	79.4773	715	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016763475.1	s__Roseicyclus sp016763475	78.7764	494	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	78.356	545	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689745.1	s__Roseicyclus sp015689745	78.3158	497	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155465.1	s__Alterinioella nitratireducens	78.0654	438	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Alterinioella	95.0	97.91	97.83	0.91	0.91	3	-
GCF_000590925.1	s__Roseicyclus elongatus	78.0401	494	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148775.1	s__Roseicyclus mahoneyensis	77.9029	465	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003688285.1	s__Rhodophyticola porphyridii	77.8042	388	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodophyticola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015689705.1	s__HKCCE3408 sp015689705	77.6255	360	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HKCCE3408	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001634885.1	s__Sulfitobacter sp001634885	77.3034	234	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.85	95.06	0.84	0.78	4	-
GCF_900111315.1	s__Tranquillimonas rosea	76.9338	281	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176485.1	s__Primorskyibacter flagellatus_A	76.93	238	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007125415.1	s__Roseovarius sp007125415	76.6242	128	1440	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	98.93	98.93	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:24,229] [INFO] GTDB search result was written to GCF_019195455.1_ASM1919545v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:24,230] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:24,234] [INFO] DFAST_QC result json was written to GCF_019195455.1_ASM1919545v2_genomic.fna/dqc_result.json
[2024-01-24 11:36:24,234] [INFO] DFAST_QC completed!
[2024-01-24 11:36:24,234] [INFO] Total running time: 0h1m41s