[2024-01-24 12:05:26,606] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:05:26,607] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:05:26,608] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c473735-1671-46c4-ae26-f701fc2c9b5a/dqc_reference
[2024-01-24 12:05:30,677] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:05:30,678] [INFO] Task started: Prodigal
[2024-01-24 12:05:30,679] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6860ad6-0ec4-42b0-841b-312fd42a6e14/GCF_003719295.1_ASM371929v1_genomic.fna.gz | prodigal -d GCF_003719295.1_ASM371929v1_genomic.fna/cds.fna -a GCF_003719295.1_ASM371929v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:05:43,870] [INFO] Task succeeded: Prodigal
[2024-01-24 12:05:43,871] [INFO] Task started: HMMsearch
[2024-01-24 12:05:43,871] [INFO] Running command: hmmsearch --tblout GCF_003719295.1_ASM371929v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c473735-1671-46c4-ae26-f701fc2c9b5a/dqc_reference/reference_markers.hmm GCF_003719295.1_ASM371929v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:05:44,175] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:05:44,176] [INFO] Found 6/6 markers.
[2024-01-24 12:05:44,216] [INFO] Query marker FASTA was written to GCF_003719295.1_ASM371929v1_genomic.fna/markers.fasta
[2024-01-24 12:05:44,217] [INFO] Task started: Blastn
[2024-01-24 12:05:44,217] [INFO] Running command: blastn -query GCF_003719295.1_ASM371929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c473735-1671-46c4-ae26-f701fc2c9b5a/dqc_reference/reference_markers.fasta -out GCF_003719295.1_ASM371929v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:05:44,996] [INFO] Task succeeded: Blastn
[2024-01-24 12:05:45,002] [INFO] Selected 15 target genomes.
[2024-01-24 12:05:45,002] [INFO] Target genome list was writen to GCF_003719295.1_ASM371929v1_genomic.fna/target_genomes.txt
[2024-01-24 12:05:45,015] [INFO] Task started: fastANI
[2024-01-24 12:05:45,016] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6860ad6-0ec4-42b0-841b-312fd42a6e14/GCF_003719295.1_ASM371929v1_genomic.fna.gz --refList GCF_003719295.1_ASM371929v1_genomic.fna/target_genomes.txt --output GCF_003719295.1_ASM371929v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:05:57,161] [INFO] Task succeeded: fastANI
[2024-01-24 12:05:57,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c473735-1671-46c4-ae26-f701fc2c9b5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:05:57,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c473735-1671-46c4-ae26-f701fc2c9b5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:05:57,174] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:05:57,174] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:05:57,175] [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
Haliea alexandrii	strain=LZ-16-2	GCA_003719295.1	2448162	2448162	type	True	100.0	1315	1315	95	conclusive
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	93.2017	1095	1315	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	78.7573	400	1315	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	78.2056	332	1315	95	below_threshold
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	77.9481	345	1315	95	below_threshold
Kineobactrum sediminis	strain=F02	GCA_002868715.1	1905677	1905677	type	True	77.9263	320	1315	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	77.8102	309	1315	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	77.3723	290	1315	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	77.0684	236	1315	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	76.887	96	1315	95	below_threshold
Pseudomonas kuykendallii	strain=NRRL B-59562	GCA_900106975.1	1007099	1007099	type	True	76.5628	110	1315	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	76.5258	94	1315	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.4737	122	1315	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.3929	113	1315	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	76.0161	69	1315	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:05:57,176] [INFO] DFAST Taxonomy check result was written to GCF_003719295.1_ASM371929v1_genomic.fna/tc_result.tsv
[2024-01-24 12:05:57,177] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:05:57,177] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:05:57,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c473735-1671-46c4-ae26-f701fc2c9b5a/dqc_reference/checkm_data
[2024-01-24 12:05:57,178] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:05:57,222] [INFO] Task started: CheckM
[2024-01-24 12:05:57,222] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003719295.1_ASM371929v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003719295.1_ASM371929v1_genomic.fna/checkm_input GCF_003719295.1_ASM371929v1_genomic.fna/checkm_result
[2024-01-24 12:06:37,477] [INFO] Task succeeded: CheckM
[2024-01-24 12:06:37,479] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:06:37,501] [INFO] ===== Completeness check finished =====
[2024-01-24 12:06:37,501] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:06:37,502] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003719295.1_ASM371929v1_genomic.fna/markers.fasta)
[2024-01-24 12:06:37,502] [INFO] Task started: Blastn
[2024-01-24 12:06:37,503] [INFO] Running command: blastn -query GCF_003719295.1_ASM371929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c473735-1671-46c4-ae26-f701fc2c9b5a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003719295.1_ASM371929v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:38,854] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:38,859] [INFO] Selected 8 target genomes.
[2024-01-24 12:06:38,859] [INFO] Target genome list was writen to GCF_003719295.1_ASM371929v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:06:38,865] [INFO] Task started: fastANI
[2024-01-24 12:06:38,866] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6860ad6-0ec4-42b0-841b-312fd42a6e14/GCF_003719295.1_ASM371929v1_genomic.fna.gz --refList GCF_003719295.1_ASM371929v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003719295.1_ASM371929v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:06:46,015] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:46,022] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:06:46,023] [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_003719295.1	s__Haliea alexandrii	100.0	1315	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000423125.1	s__Haliea salexigens	93.2017	1095	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	96.91	96.59	0.87	0.83	15	-
GCA_002416125.1	s__Haliea sp002416125	81.5862	835	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.96	99.96	0.96	0.96	2	-
GCA_002414665.1	s__Haliea sp002414665	81.564	855	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Haliea	95.0	99.89	99.89	0.97	0.97	2	-
GCA_002699145.1	s__Halioglobus sp002699145	78.6831	317	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCA_002692965.1	s__NZNC01 sp002692965	78.526	396	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__NZNC01	95.0	98.60	97.22	0.91	0.84	3	-
GCF_010669285.1	s__Kineobactrum salinum	78.2056	332	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064635.1	s__Parahaliea aestuarii	77.9481	345	1315	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:06:46,024] [INFO] GTDB search result was written to GCF_003719295.1_ASM371929v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:06:46,026] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:06:46,030] [INFO] DFAST_QC result json was written to GCF_003719295.1_ASM371929v1_genomic.fna/dqc_result.json
[2024-01-24 12:06:46,031] [INFO] DFAST_QC completed!
[2024-01-24 12:06:46,031] [INFO] Total running time: 0h1m19s