[2024-01-25 18:06:35,590] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:35,596] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:35,596] [INFO] DQC Reference Directory: /var/lib/cwl/stg167fad48-a026-4cb5-b50d-606baeb189d9/dqc_reference
[2024-01-25 18:06:36,789] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:36,790] [INFO] Task started: Prodigal
[2024-01-25 18:06:36,790] [INFO] Running command: gunzip -c /var/lib/cwl/stg98273fb1-1f6b-46d8-99d3-fe81116e79fd/GCF_014640195.1_ASM1464019v1_genomic.fna.gz | prodigal -d GCF_014640195.1_ASM1464019v1_genomic.fna/cds.fna -a GCF_014640195.1_ASM1464019v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:46,017] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:46,017] [INFO] Task started: HMMsearch
[2024-01-25 18:06:46,017] [INFO] Running command: hmmsearch --tblout GCF_014640195.1_ASM1464019v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg167fad48-a026-4cb5-b50d-606baeb189d9/dqc_reference/reference_markers.hmm GCF_014640195.1_ASM1464019v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:46,245] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:46,246] [INFO] Found 6/6 markers.
[2024-01-25 18:06:46,271] [INFO] Query marker FASTA was written to GCF_014640195.1_ASM1464019v1_genomic.fna/markers.fasta
[2024-01-25 18:06:46,271] [INFO] Task started: Blastn
[2024-01-25 18:06:46,271] [INFO] Running command: blastn -query GCF_014640195.1_ASM1464019v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg167fad48-a026-4cb5-b50d-606baeb189d9/dqc_reference/reference_markers.fasta -out GCF_014640195.1_ASM1464019v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:46,869] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:46,872] [INFO] Selected 24 target genomes.
[2024-01-25 18:06:46,872] [INFO] Target genome list was writen to GCF_014640195.1_ASM1464019v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:46,888] [INFO] Task started: fastANI
[2024-01-25 18:06:46,888] [INFO] Running command: fastANI --query /var/lib/cwl/stg98273fb1-1f6b-46d8-99d3-fe81116e79fd/GCF_014640195.1_ASM1464019v1_genomic.fna.gz --refList GCF_014640195.1_ASM1464019v1_genomic.fna/target_genomes.txt --output GCF_014640195.1_ASM1464019v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:07:00,907] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:00,908] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg167fad48-a026-4cb5-b50d-606baeb189d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:07:00,908] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg167fad48-a026-4cb5-b50d-606baeb189d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:07:00,921] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:07:00,921] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:07:00,921] [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
Psychroflexus planctonicus	strain=CGMCC 1.12931	GCA_014640195.1	1526575	1526575	type	True	100.0	1019	1022	95	conclusive
Psychroflexus salis	strain=CGMCC 1.12925	GCA_014640175.1	1526574	1526574	type	True	80.125	586	1022	95	below_threshold
Psychroflexus maritimus	strain=C1	GCA_011089875.1	2714865	2714865	type	True	78.0561	209	1022	95	below_threshold
Psychroflexus salarius	strain=DSM 25661	GCA_900129035.1	1155689	1155689	type	True	77.7132	148	1022	95	below_threshold
Mesonia phycicola	strain=DSM 21425	GCA_900141885.1	579105	579105	type	True	76.6226	112	1022	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	76.5624	76	1022	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	76.5624	76	1022	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.5479	78	1022	95	below_threshold
Psychroflexus halocasei	strain=DSM 23581	GCA_900107595.1	908615	908615	type	True	76.4593	101	1022	95	below_threshold
Haloflavibacter putidus	strain=PLHSN227	GCA_006546625.1	2576776	2576776	type	True	76.4456	104	1022	95	below_threshold
Mesonia algae	strain=DSM 15361	GCA_003253545.1	213248	213248	type	True	76.4276	109	1022	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.3263	83	1022	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	76.3091	78	1022	95	below_threshold
Mesonia oceanica	strain=ISS653	GCA_902499555.1	2687242	2687242	type	True	76.3076	129	1022	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	76.2512	82	1022	95	below_threshold
Kordia antarctica	strain=IMCC3317	GCA_009901525.1	1218801	1218801	type	True	76.2302	79	1022	95	below_threshold
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	76.1575	69	1022	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	76.1431	64	1022	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.012	78	1022	95	below_threshold
Mesohalobacter halotolerans	strain=WDS2C27	GCA_006120725.1	1883405	1883405	type	True	76.0082	105	1022	95	below_threshold
Salegentibacter lacus	strain=LM13S	GCA_020164555.1	2873599	2873599	type	True	75.9658	73	1022	95	below_threshold
Flavobacterium channae	strain=KSM-R2A30	GCA_021172165.1	2897181	2897181	type	True	75.9257	82	1022	95	below_threshold
Flavobacterium profundi	strain=TP390	GCA_009753805.1	1774945	1774945	type	True	75.8166	73	1022	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:07:00,923] [INFO] DFAST Taxonomy check result was written to GCF_014640195.1_ASM1464019v1_genomic.fna/tc_result.tsv
[2024-01-25 18:07:00,923] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:07:00,923] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:07:00,924] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg167fad48-a026-4cb5-b50d-606baeb189d9/dqc_reference/checkm_data
[2024-01-25 18:07:00,924] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:07:00,956] [INFO] Task started: CheckM
[2024-01-25 18:07:00,956] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640195.1_ASM1464019v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640195.1_ASM1464019v1_genomic.fna/checkm_input GCF_014640195.1_ASM1464019v1_genomic.fna/checkm_result
[2024-01-25 18:07:31,268] [INFO] Task succeeded: CheckM
[2024-01-25 18:07:31,269] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:07:31,287] [INFO] ===== Completeness check finished =====
[2024-01-25 18:07:31,287] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:07:31,288] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640195.1_ASM1464019v1_genomic.fna/markers.fasta)
[2024-01-25 18:07:31,288] [INFO] Task started: Blastn
[2024-01-25 18:07:31,288] [INFO] Running command: blastn -query GCF_014640195.1_ASM1464019v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg167fad48-a026-4cb5-b50d-606baeb189d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640195.1_ASM1464019v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:07:32,136] [INFO] Task succeeded: Blastn
[2024-01-25 18:07:32,139] [INFO] Selected 20 target genomes.
[2024-01-25 18:07:32,139] [INFO] Target genome list was writen to GCF_014640195.1_ASM1464019v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:07:32,157] [INFO] Task started: fastANI
[2024-01-25 18:07:32,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg98273fb1-1f6b-46d8-99d3-fe81116e79fd/GCF_014640195.1_ASM1464019v1_genomic.fna.gz --refList GCF_014640195.1_ASM1464019v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640195.1_ASM1464019v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:07:43,906] [INFO] Task succeeded: fastANI
[2024-01-25 18:07:43,918] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:07:43,918] [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_014640195.1	s__Psychroflexus planctonicus	100.0	1019	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014640175.1	s__Psychroflexus salis	80.1367	585	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011089875.1	s__Psychroflexus maritimus	78.0561	209	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003564185.1	s__Psychroflexus sp003564185	77.1432	149	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	76.5624	76	1022	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_013249065.1	s__Winogradskyella litoriviva	76.5479	78	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011777505.1	s__CAU-1491 sp011777505	76.5184	76	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423405.1	s__Mesonia mobilis	76.4679	124	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900107595.1	s__Psychroflexus halocasei	76.4593	101	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	95.19	95.19	0.87	0.87	2	-
GCA_006546625.1	s__Mesonia sp006546625	76.4456	104	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253545.1	s__Mesonia algae	76.4276	109	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	95.16	95.16	0.83	0.83	2	-
GCA_007116535.1	s__Psychroflexus sp007116535	76.4	79	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902499555.1	s__Mesonia oceanica	76.3076	129	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mesonia	95.0	99.91	99.87	0.96	0.92	8	-
GCF_900115185.1	s__Algorimicrobium echini	76.2848	79	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algorimicrobium	95.0	97.77	97.77	0.81	0.81	2	-
GCA_003565575.1	s__Psychroflexus sp003565575	76.2754	99	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112595.1	s__Algibacter_B pectinivorans	76.2512	82	1022	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_009901525.1	s__Kordia antarctica	76.2302	79	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Kordia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008084905.1	s__Xanthomarina maritima	75.9938	98	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Xanthomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050675.1	s__Maribacter sp011050675	75.7672	57	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002482975.1	s__Flavobacterium sp002482975	75.3777	67	1022	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:07:43,920] [INFO] GTDB search result was written to GCF_014640195.1_ASM1464019v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:07:43,920] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:07:43,924] [INFO] DFAST_QC result json was written to GCF_014640195.1_ASM1464019v1_genomic.fna/dqc_result.json
[2024-01-25 18:07:43,924] [INFO] DFAST_QC completed!
[2024-01-25 18:07:43,924] [INFO] Total running time: 0h1m8s