[2024-01-24 13:17:58,774] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:58,778] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:58,778] [INFO] DQC Reference Directory: /var/lib/cwl/stg92c41ac2-9c1f-4cbd-b95d-232b33f34028/dqc_reference
[2024-01-24 13:18:00,097] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:00,098] [INFO] Task started: Prodigal
[2024-01-24 13:18:00,098] [INFO] Running command: gunzip -c /var/lib/cwl/stg45986b4a-9b17-46fb-becb-a239545e822b/GCF_020523965.1_ASM2052396v1_genomic.fna.gz | prodigal -d GCF_020523965.1_ASM2052396v1_genomic.fna/cds.fna -a GCF_020523965.1_ASM2052396v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:11,379] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:11,379] [INFO] Task started: HMMsearch
[2024-01-24 13:18:11,379] [INFO] Running command: hmmsearch --tblout GCF_020523965.1_ASM2052396v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92c41ac2-9c1f-4cbd-b95d-232b33f34028/dqc_reference/reference_markers.hmm GCF_020523965.1_ASM2052396v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:11,671] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:11,672] [INFO] Found 6/6 markers.
[2024-01-24 13:18:11,706] [INFO] Query marker FASTA was written to GCF_020523965.1_ASM2052396v1_genomic.fna/markers.fasta
[2024-01-24 13:18:11,707] [INFO] Task started: Blastn
[2024-01-24 13:18:11,707] [INFO] Running command: blastn -query GCF_020523965.1_ASM2052396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92c41ac2-9c1f-4cbd-b95d-232b33f34028/dqc_reference/reference_markers.fasta -out GCF_020523965.1_ASM2052396v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:12,434] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:12,438] [INFO] Selected 19 target genomes.
[2024-01-24 13:18:12,438] [INFO] Target genome list was writen to GCF_020523965.1_ASM2052396v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:12,465] [INFO] Task started: fastANI
[2024-01-24 13:18:12,465] [INFO] Running command: fastANI --query /var/lib/cwl/stg45986b4a-9b17-46fb-becb-a239545e822b/GCF_020523965.1_ASM2052396v1_genomic.fna.gz --refList GCF_020523965.1_ASM2052396v1_genomic.fna/target_genomes.txt --output GCF_020523965.1_ASM2052396v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:26,411] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:26,411] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92c41ac2-9c1f-4cbd-b95d-232b33f34028/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:26,411] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92c41ac2-9c1f-4cbd-b95d-232b33f34028/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:26,429] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:18:26,429] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:18:26,429] [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
Tamlana sedimentorum	strain=JCM 19808	GCA_000943565.1	1435349	1435349	type	True	90.3174	995	1194	95	below_threshold
Tamlana nanhaiensis	strain=FHC16	GCA_000943555.1	1382798	1382798	type	True	83.8559	791	1194	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	79.7865	467	1194	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	78.592	471	1194	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.3518	503	1194	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	78.3309	495	1194	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	78.323	496	1194	95	below_threshold
Tamlana agarivorans	strain=JW-26	GCA_001642835.1	481183	481183	type	True	78.1274	323	1194	95	below_threshold
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	78.1158	459	1194	95	below_threshold
Aestuariibaculum marinum	strain=IP7	GCA_014596975.1	2683592	2683592	type	True	78.0837	333	1194	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.9562	317	1194	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	77.8931	326	1194	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.8264	338	1194	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.7888	320	1194	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.7629	228	1194	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	77.7002	257	1194	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.5753	293	1194	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.4239	229	1194	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	77.2442	203	1194	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:26,431] [INFO] DFAST Taxonomy check result was written to GCF_020523965.1_ASM2052396v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:26,432] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:26,432] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:26,432] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92c41ac2-9c1f-4cbd-b95d-232b33f34028/dqc_reference/checkm_data
[2024-01-24 13:18:26,433] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:26,483] [INFO] Task started: CheckM
[2024-01-24 13:18:26,483] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020523965.1_ASM2052396v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020523965.1_ASM2052396v1_genomic.fna/checkm_input GCF_020523965.1_ASM2052396v1_genomic.fna/checkm_result
[2024-01-24 13:19:02,452] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:02,453] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:02,470] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:02,470] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:02,471] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020523965.1_ASM2052396v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:02,471] [INFO] Task started: Blastn
[2024-01-24 13:19:02,471] [INFO] Running command: blastn -query GCF_020523965.1_ASM2052396v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92c41ac2-9c1f-4cbd-b95d-232b33f34028/dqc_reference/reference_markers_gtdb.fasta -out GCF_020523965.1_ASM2052396v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:03,506] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:03,510] [INFO] Selected 17 target genomes.
[2024-01-24 13:19:03,510] [INFO] Target genome list was writen to GCF_020523965.1_ASM2052396v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:03,534] [INFO] Task started: fastANI
[2024-01-24 13:19:03,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg45986b4a-9b17-46fb-becb-a239545e822b/GCF_020523965.1_ASM2052396v1_genomic.fna.gz --refList GCF_020523965.1_ASM2052396v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020523965.1_ASM2052396v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:18,304] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:18,319] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:19:18,320] [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_000943565.1	s__Tamlana_B sedimentorum	90.3015	996	1194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000943555.1	s__Tamlana_B nanhaiensis	83.8986	789	1194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	79.7862	467	1194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112595.1	s__Algibacter_B pectinivorans	78.5877	472	1194	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_003143755.1	s__Algibacter_B sp003143755	78.5624	408	1194	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_000941055.1	s__Siansivirga zeaxanthinifaciens	78.4017	388	1194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Siansivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	78.3546	502	1194	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_000789235.1	s__Wocania ichthyoenteri	78.3202	417	1194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033385.1	s__Algibacter pacificus	78.3135	396	1194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001642835.1	s__Tamlana_A agarivorans	78.134	323	1194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	95.46	95.44	0.83	0.81	3	-
GCA_900112395.1	s__Algibacter lectus	78.1158	459	1194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	98.81	98.79	0.90	0.89	6	-
GCF_004341235.1	s__Mariniflexile fucanivorans	78.0934	411	1194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003425985.1	s__Mariniflexile sp002848895	77.926	357	1194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	99.99	99.99	1.00	1.00	2	-
GCF_008806375.1	s__Tamlana_A haliotis	77.9051	324	1194	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_000425645.1	s__Gaetbulibacter saemankumensis	77.851	282	1194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Gaetbulibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007827365.1	s__Olleya sp002323495	77.3149	268	1194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Olleya	95.0	96.78	96.78	0.90	0.90	2	-
GCF_000348685.1	s__Xanthomarina gelatinilytica	77.2641	201	1194	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	98.37	98.31	0.90	0.88	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:18,322] [INFO] GTDB search result was written to GCF_020523965.1_ASM2052396v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:18,322] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:18,327] [INFO] DFAST_QC result json was written to GCF_020523965.1_ASM2052396v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:18,327] [INFO] DFAST_QC completed!
[2024-01-24 13:19:18,327] [INFO] Total running time: 0h1m20s