[2024-01-24 14:55:51,297] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:51,299] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:51,299] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a10b050-0643-4ef3-aef4-1aa742dd5be8/dqc_reference
[2024-01-24 14:55:52,619] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:52,620] [INFO] Task started: Prodigal
[2024-01-24 14:55:52,620] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d5f3e69-05ad-4c9e-bb9e-64037127140a/GCF_006265225.1_ASM626522v1_genomic.fna.gz | prodigal -d GCF_006265225.1_ASM626522v1_genomic.fna/cds.fna -a GCF_006265225.1_ASM626522v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:06,348] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:06,349] [INFO] Task started: HMMsearch
[2024-01-24 14:56:06,349] [INFO] Running command: hmmsearch --tblout GCF_006265225.1_ASM626522v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a10b050-0643-4ef3-aef4-1aa742dd5be8/dqc_reference/reference_markers.hmm GCF_006265225.1_ASM626522v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:06,652] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:06,654] [INFO] Found 6/6 markers.
[2024-01-24 14:56:06,692] [INFO] Query marker FASTA was written to GCF_006265225.1_ASM626522v1_genomic.fna/markers.fasta
[2024-01-24 14:56:06,693] [INFO] Task started: Blastn
[2024-01-24 14:56:06,693] [INFO] Running command: blastn -query GCF_006265225.1_ASM626522v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a10b050-0643-4ef3-aef4-1aa742dd5be8/dqc_reference/reference_markers.fasta -out GCF_006265225.1_ASM626522v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:07,389] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:07,392] [INFO] Selected 23 target genomes.
[2024-01-24 14:56:07,392] [INFO] Target genome list was writen to GCF_006265225.1_ASM626522v1_genomic.fna/target_genomes.txt
[2024-01-24 14:56:07,403] [INFO] Task started: fastANI
[2024-01-24 14:56:07,403] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d5f3e69-05ad-4c9e-bb9e-64037127140a/GCF_006265225.1_ASM626522v1_genomic.fna.gz --refList GCF_006265225.1_ASM626522v1_genomic.fna/target_genomes.txt --output GCF_006265225.1_ASM626522v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:23,091] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:23,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a10b050-0643-4ef3-aef4-1aa742dd5be8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:23,092] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a10b050-0643-4ef3-aef4-1aa742dd5be8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:23,109] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:56:23,109] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:56:23,109] [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
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	78.4797	379	1307	95	below_threshold
Algibacter mikhailovii	strain=KCTC 12710	GCA_014651495.1	425498	425498	type	True	78.4665	392	1307	95	below_threshold
Tamlana carrageenivorans	strain=UJ94	GCA_002893765.1	2069432	2069432	type	True	78.438	353	1307	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.4286	385	1307	95	below_threshold
Algibacter onchidii	strain=XY-114	GCA_004804355.1	2562860	2562860	type	True	78.3659	429	1307	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	78.3638	403	1307	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	78.1924	348	1307	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	78.1884	387	1307	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	78.1375	405	1307	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	78.1276	345	1307	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.1186	402	1307	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	78.0857	374	1307	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.9458	290	1307	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	77.9043	361	1307	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	77.8831	283	1307	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.879	301	1307	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	77.8708	332	1307	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.8595	372	1307	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.8447	211	1307	95	below_threshold
Tamlana nanhaiensis	strain=FHC16	GCA_000943555.1	1382798	1382798	type	True	77.8231	329	1307	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.727	310	1307	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	77.5317	306	1307	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	77.4785	251	1307	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:23,111] [INFO] DFAST Taxonomy check result was written to GCF_006265225.1_ASM626522v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:23,112] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:23,112] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:23,112] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a10b050-0643-4ef3-aef4-1aa742dd5be8/dqc_reference/checkm_data
[2024-01-24 14:56:23,113] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:23,168] [INFO] Task started: CheckM
[2024-01-24 14:56:23,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006265225.1_ASM626522v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006265225.1_ASM626522v1_genomic.fna/checkm_input GCF_006265225.1_ASM626522v1_genomic.fna/checkm_result
[2024-01-24 14:57:05,703] [INFO] Task succeeded: CheckM
[2024-01-24 14:57:05,704] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:57:05,721] [INFO] ===== Completeness check finished =====
[2024-01-24 14:57:05,721] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:57:05,722] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006265225.1_ASM626522v1_genomic.fna/markers.fasta)
[2024-01-24 14:57:05,722] [INFO] Task started: Blastn
[2024-01-24 14:57:05,722] [INFO] Running command: blastn -query GCF_006265225.1_ASM626522v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a10b050-0643-4ef3-aef4-1aa742dd5be8/dqc_reference/reference_markers_gtdb.fasta -out GCF_006265225.1_ASM626522v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:57:06,686] [INFO] Task succeeded: Blastn
[2024-01-24 14:57:06,689] [INFO] Selected 20 target genomes.
[2024-01-24 14:57:06,689] [INFO] Target genome list was writen to GCF_006265225.1_ASM626522v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:57:06,731] [INFO] Task started: fastANI
[2024-01-24 14:57:06,732] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d5f3e69-05ad-4c9e-bb9e-64037127140a/GCF_006265225.1_ASM626522v1_genomic.fna.gz --refList GCF_006265225.1_ASM626522v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006265225.1_ASM626522v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:57:21,180] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:21,200] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:57:21,201] [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_006265225.1	s__Tamlana_C fucoidanivorans	100.0	1306	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_C	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014651495.1	s__Algibacter_E mikhailovii	78.446	392	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	78.439	384	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002893765.1	s__Tamlana_A carrageenivorans	78.4249	354	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	78.3897	401	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004804355.1	s__Tamlana_C sp004804355	78.3688	430	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860245.1	s__Tamlana_A agarivorans_A	78.3362	371	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015355625.1	s__Tamlana_A sp015355625	78.3225	410	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	78.3025	426	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806375.1	s__Tamlana_A haliotis	78.2094	347	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	78.1978	380	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	78.1012	372	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	78.0948	406	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_008056315.1	s__Seonamhaeicola maritimus	78.0941	373	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004310335.1	s__Jejuia pacifica	78.0189	315	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000425645.1	s__Gaetbulibacter saemankumensis	77.9654	302	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gaetbulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	77.8727	373	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480415.1	s__Algibacter_B sp905480415	77.8677	307	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002973595.1	s__Jejuia pallidilutea	77.7682	320	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	98.03	97.97	0.83	0.83	4	-
GCF_018860825.1	s__Oceanihabitans sp018860825	77.5133	258	1307	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:57:21,202] [INFO] GTDB search result was written to GCF_006265225.1_ASM626522v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:57:21,203] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:57:21,207] [INFO] DFAST_QC result json was written to GCF_006265225.1_ASM626522v1_genomic.fna/dqc_result.json
[2024-01-24 14:57:21,207] [INFO] DFAST_QC completed!
[2024-01-24 14:57:21,207] [INFO] Total running time: 0h1m30s