[2023-06-19 08:50:06,904] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:50:06,907] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:50:06,908] [INFO] DQC Reference Directory: /var/lib/cwl/stg0215f954-53f6-4f32-820a-9930bd2af8da/dqc_reference
[2023-06-19 08:50:08,106] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:50:08,107] [INFO] Task started: Prodigal
[2023-06-19 08:50:08,107] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a1bc38e-39a7-4d58-a7e4-c6625d98709f/GCA_013042595.1_ASM1304259v1_genomic.fna.gz | prodigal -d GCA_013042595.1_ASM1304259v1_genomic.fna/cds.fna -a GCA_013042595.1_ASM1304259v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:50:20,115] [INFO] Task succeeded: Prodigal
[2023-06-19 08:50:20,116] [INFO] Task started: HMMsearch
[2023-06-19 08:50:20,116] [INFO] Running command: hmmsearch --tblout GCA_013042595.1_ASM1304259v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0215f954-53f6-4f32-820a-9930bd2af8da/dqc_reference/reference_markers.hmm GCA_013042595.1_ASM1304259v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:50:20,319] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:50:20,320] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0a1bc38e-39a7-4d58-a7e4-c6625d98709f/GCA_013042595.1_ASM1304259v1_genomic.fna.gz]
[2023-06-19 08:50:20,348] [INFO] Query marker FASTA was written to GCA_013042595.1_ASM1304259v1_genomic.fna/markers.fasta
[2023-06-19 08:50:20,349] [INFO] Task started: Blastn
[2023-06-19 08:50:20,349] [INFO] Running command: blastn -query GCA_013042595.1_ASM1304259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0215f954-53f6-4f32-820a-9930bd2af8da/dqc_reference/reference_markers.fasta -out GCA_013042595.1_ASM1304259v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:50:20,923] [INFO] Task succeeded: Blastn
[2023-06-19 08:50:20,927] [INFO] Selected 28 target genomes.
[2023-06-19 08:50:20,928] [INFO] Target genome list was writen to GCA_013042595.1_ASM1304259v1_genomic.fna/target_genomes.txt
[2023-06-19 08:50:20,929] [INFO] Task started: fastANI
[2023-06-19 08:50:20,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a1bc38e-39a7-4d58-a7e4-c6625d98709f/GCA_013042595.1_ASM1304259v1_genomic.fna.gz --refList GCA_013042595.1_ASM1304259v1_genomic.fna/target_genomes.txt --output GCA_013042595.1_ASM1304259v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:50:36,202] [INFO] Task succeeded: fastANI
[2023-06-19 08:50:36,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0215f954-53f6-4f32-820a-9930bd2af8da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:50:36,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0215f954-53f6-4f32-820a-9930bd2af8da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:50:36,213] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:50:36,213] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 08:50:36,213] [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
Pukyongia salina	strain=RR4-38	GCA_002966125.1	2094025	2094025	type	True	78.702	353	956	95	below_threshold
Constantimarinum furrinae	strain=ALE3EI	GCA_014295415.1	2562285	2562285	type	True	77.1854	136	956	95	below_threshold
Altibacter lentus	strain=JLT2010	GCA_000746845.1	1223410	1223410	type	True	77.0412	98	956	95	below_threshold
Luteirhabdus pelagi	strain=A3-108	GCA_016827595.1	2792783	2792783	type	True	76.9129	69	956	95	below_threshold
Cochleicola gelatinilyticus	strain=LPB0005	GCA_001637325.1	1763537	1763537	type	True	76.788	75	956	95	below_threshold
Marinirhabdus gelatinilytica	strain=DSM 101478	GCA_003353425.1	1703343	1703343	type	True	76.7768	80	956	95	below_threshold
Ulvibacter litoralis	strain=DSM 16195	GCA_900102055.1	227084	227084	type	True	76.7439	73	956	95	below_threshold
Ulvibacter litoralis	strain=KCTC 12104	GCA_014651275.1	227084	227084	type	True	76.7393	75	956	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	76.6836	61	956	95	below_threshold
Marixanthomonas ophiurae	strain=KMM 3046	GCA_003413745.1	387659	387659	type	True	76.4271	87	956	95	below_threshold
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	76.3211	93	956	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:50:36,215] [INFO] DFAST Taxonomy check result was written to GCA_013042595.1_ASM1304259v1_genomic.fna/tc_result.tsv
[2023-06-19 08:50:36,215] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:50:36,216] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:50:36,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0215f954-53f6-4f32-820a-9930bd2af8da/dqc_reference/checkm_data
[2023-06-19 08:50:36,217] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:50:36,247] [INFO] Task started: CheckM
[2023-06-19 08:50:36,247] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013042595.1_ASM1304259v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013042595.1_ASM1304259v1_genomic.fna/checkm_input GCA_013042595.1_ASM1304259v1_genomic.fna/checkm_result
[2023-06-19 08:51:14,218] [INFO] Task succeeded: CheckM
[2023-06-19 08:51:14,219] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.53%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:51:14,237] [INFO] ===== Completeness check finished =====
[2023-06-19 08:51:14,237] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:51:14,238] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013042595.1_ASM1304259v1_genomic.fna/markers.fasta)
[2023-06-19 08:51:14,238] [INFO] Task started: Blastn
[2023-06-19 08:51:14,238] [INFO] Running command: blastn -query GCA_013042595.1_ASM1304259v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0215f954-53f6-4f32-820a-9930bd2af8da/dqc_reference/reference_markers_gtdb.fasta -out GCA_013042595.1_ASM1304259v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:51:14,987] [INFO] Task succeeded: Blastn
[2023-06-19 08:51:14,992] [INFO] Selected 20 target genomes.
[2023-06-19 08:51:14,992] [INFO] Target genome list was writen to GCA_013042595.1_ASM1304259v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:51:14,999] [INFO] Task started: fastANI
[2023-06-19 08:51:14,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a1bc38e-39a7-4d58-a7e4-c6625d98709f/GCA_013042595.1_ASM1304259v1_genomic.fna.gz --refList GCA_013042595.1_ASM1304259v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013042595.1_ASM1304259v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:51:26,771] [INFO] Task succeeded: fastANI
[2023-06-19 08:51:26,784] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 08:51:26,785] [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_013043685.1	s__Pukyongia sp013043685	99.8255	914	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	99.85	99.75	0.96	0.95	6	conclusive
GCF_002966125.1	s__Pukyongia salina	78.702	353	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008501705.1	s__Pukyongia sp008501705	78.4671	328	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479745.1	s__Pukyongia sp905479745	78.4149	315	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pukyongia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014295415.1	s__Altibacter sp014295415	77.1854	136	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009827225.1	s__SMXJ01 sp009827225	77.1258	117	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SMXJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000746845.1	s__Altibacter lentus	77.0412	98	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002696485.1	s__Altibacter sp002696485	77.0353	93	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Altibacter	95.0	99.86	99.86	0.91	0.91	2	-
GCF_003333325.1	s__Ulvibacter_A alkanivorans	76.9539	99	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacter_A	95.0	98.51	98.51	0.88	0.88	2	-
GCA_002375495.1	s__Marinirhabdus sp002375495	76.8237	77	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.31	97.88	0.90	0.71	8	-
GCF_003353425.1	s__Marinirhabdus gelatinilytica	76.8041	79	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364215.1	s__Aequorivita sp002364215	76.516	78	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.66	98.55	0.97	0.89	12	-
GCF_900489465.1	s__Aequorivita sp900489465	76.495	73	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003413745.1	s__Marixanthomonas ophiurae	76.4271	87	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marixanthomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002337605.1	s__Marinirhabdus sp002337605	76.3882	95	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Marinirhabdus	95.0	98.69	98.69	0.95	0.95	2	-
GCF_001573155.1	s__Aequorivita aquimaris	76.2913	92	956	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 08:51:26,786] [INFO] GTDB search result was written to GCA_013042595.1_ASM1304259v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:51:26,788] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:51:26,792] [INFO] DFAST_QC result json was written to GCA_013042595.1_ASM1304259v1_genomic.fna/dqc_result.json
[2023-06-19 08:51:26,792] [INFO] DFAST_QC completed!
[2023-06-19 08:51:26,792] [INFO] Total running time: 0h1m20s