[2024-01-25 19:06:50,549] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:06:50,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:06:50,551] [INFO] DQC Reference Directory: /var/lib/cwl/stg7fdbce49-0a42-4232-94fc-b3306433f901/dqc_reference
[2024-01-25 19:06:51,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:06:51,675] [INFO] Task started: Prodigal
[2024-01-25 19:06:51,675] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d99050c-c6d9-4e69-97fd-005dcdc7880b/GCF_030295935.1_ASM3029593v1_genomic.fna.gz | prodigal -d GCF_030295935.1_ASM3029593v1_genomic.fna/cds.fna -a GCF_030295935.1_ASM3029593v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:06:58,014] [INFO] Task succeeded: Prodigal
[2024-01-25 19:06:58,015] [INFO] Task started: HMMsearch
[2024-01-25 19:06:58,015] [INFO] Running command: hmmsearch --tblout GCF_030295935.1_ASM3029593v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7fdbce49-0a42-4232-94fc-b3306433f901/dqc_reference/reference_markers.hmm GCF_030295935.1_ASM3029593v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:06:58,256] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:06:58,258] [INFO] Found 6/6 markers.
[2024-01-25 19:06:58,292] [INFO] Query marker FASTA was written to GCF_030295935.1_ASM3029593v1_genomic.fna/markers.fasta
[2024-01-25 19:06:58,292] [INFO] Task started: Blastn
[2024-01-25 19:06:58,292] [INFO] Running command: blastn -query GCF_030295935.1_ASM3029593v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7fdbce49-0a42-4232-94fc-b3306433f901/dqc_reference/reference_markers.fasta -out GCF_030295935.1_ASM3029593v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:58,973] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:58,976] [INFO] Selected 18 target genomes.
[2024-01-25 19:06:58,976] [INFO] Target genome list was writen to GCF_030295935.1_ASM3029593v1_genomic.fna/target_genomes.txt
[2024-01-25 19:06:58,999] [INFO] Task started: fastANI
[2024-01-25 19:06:58,999] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d99050c-c6d9-4e69-97fd-005dcdc7880b/GCF_030295935.1_ASM3029593v1_genomic.fna.gz --refList GCF_030295935.1_ASM3029593v1_genomic.fna/target_genomes.txt --output GCF_030295935.1_ASM3029593v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:07:14,491] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:14,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7fdbce49-0a42-4232-94fc-b3306433f901/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:07:14,492] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7fdbce49-0a42-4232-94fc-b3306433f901/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:07:14,502] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:07:14,502] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:07:14,502] [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
Thalassotalea piscium	strain=DSM 26287	GCA_014207645.1	1230533	1230533	type	True	99.9449	1242	1301	95	conclusive
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	80.4109	620	1301	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	79.9493	226	1301	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	79.9355	217	1301	95	below_threshold
Moritella yayanosii	strain=DB21MT 5	GCA_900465055.1	69539	69539	type	True	78.9023	59	1301	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	78.558	181	1301	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	78.2542	221	1301	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	78.1377	83	1301	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	77.9231	205	1301	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	77.8038	227	1301	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	77.702	190	1301	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	77.5471	193	1301	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	77.5408	190	1301	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	76.5149	51	1301	95	below_threshold
Pseudoalteromonas denitrificans	strain=DSM 6059	GCA_900112265.1	43656	43656	type	True	76.4623	104	1301	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	76.2751	53	1301	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:07:14,504] [INFO] DFAST Taxonomy check result was written to GCF_030295935.1_ASM3029593v1_genomic.fna/tc_result.tsv
[2024-01-25 19:07:14,505] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:07:14,505] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:07:14,505] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7fdbce49-0a42-4232-94fc-b3306433f901/dqc_reference/checkm_data
[2024-01-25 19:07:14,506] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:07:14,545] [INFO] Task started: CheckM
[2024-01-25 19:07:14,545] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030295935.1_ASM3029593v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030295935.1_ASM3029593v1_genomic.fna/checkm_input GCF_030295935.1_ASM3029593v1_genomic.fna/checkm_result
[2024-01-25 19:07:38,494] [INFO] Task succeeded: CheckM
[2024-01-25 19:07:38,495] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:07:38,518] [INFO] ===== Completeness check finished =====
[2024-01-25 19:07:38,518] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:07:38,518] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030295935.1_ASM3029593v1_genomic.fna/markers.fasta)
[2024-01-25 19:07:38,518] [INFO] Task started: Blastn
[2024-01-25 19:07:38,518] [INFO] Running command: blastn -query GCF_030295935.1_ASM3029593v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7fdbce49-0a42-4232-94fc-b3306433f901/dqc_reference/reference_markers_gtdb.fasta -out GCF_030295935.1_ASM3029593v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:39,579] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:39,582] [INFO] Selected 18 target genomes.
[2024-01-25 19:07:39,582] [INFO] Target genome list was writen to GCF_030295935.1_ASM3029593v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:07:39,612] [INFO] Task started: fastANI
[2024-01-25 19:07:39,612] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d99050c-c6d9-4e69-97fd-005dcdc7880b/GCF_030295935.1_ASM3029593v1_genomic.fna.gz --refList GCF_030295935.1_ASM3029593v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030295935.1_ASM3029593v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:07:55,687] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:55,698] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:07:55,698] [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_014207645.1	s__Thalassotalea_B piscium	99.9449	1242	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014653195.1	s__Thalassotalea_B profundi	80.4109	620	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004295665.1	s__Litorilituus sediminis	78.7851	181	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077005.1	s__Cognaticolwellia sp014077005	78.2401	198	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.22	95.22	0.95	0.87	11	-
GCF_017168195.1	s__G2M2-11 sp017168195	78.1401	231	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__G2M2-11	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836775.1	s__Colwellia sp002836775	78.0275	196	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002000025.1	s__Cognaticolwellia aestuarii	77.9824	254	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002836255.1	s__Colwellia sp002836255	77.9541	206	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005885605.1	s__Colwellia ponticola	77.9229	204	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215385.1	s__Colwellia_A sp013215385	77.8793	218	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001913705.1	s__Thalassotalea_C sp001913705	77.8483	227	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215295.1	s__Colwellia_A sp013215295	77.7937	211	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215655.1	s__Colwellia_A sp013215655	77.7574	203	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014076845.1	s__Colwellia_A sp014076845	77.746	215	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia_A	95.0	99.15	95.49	0.95	0.86	8	-
GCF_002000085.1	s__Pseudocolwellia agarivorans	77.7355	232	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudocolwellia	95.0	95.36	95.36	0.90	0.90	2	-
GCA_015491935.1	s__GCA-2401725 sp015491935	77.6541	176	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__GCA-2401725	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003354085.1	s__Cognaticolwellia sp003354085	77.6415	204	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656435.1	s__Thalassotalea_C marina	77.549	194	1301	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Thalassotalea_C	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:07:55,699] [INFO] GTDB search result was written to GCF_030295935.1_ASM3029593v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:07:55,700] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:07:55,703] [INFO] DFAST_QC result json was written to GCF_030295935.1_ASM3029593v1_genomic.fna/dqc_result.json
[2024-01-25 19:07:55,703] [INFO] DFAST_QC completed!
[2024-01-25 19:07:55,703] [INFO] Total running time: 0h1m5s