[2024-01-25 18:10:35,695] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:10:35,697] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:10:35,697] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4409e99-3666-4292-8b8c-5f18b96d36c8/dqc_reference
[2024-01-25 18:10:36,858] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:10:36,858] [INFO] Task started: Prodigal
[2024-01-25 18:10:36,859] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd987bf3-9d3e-4e62-98e2-364af74c40a8/GCF_014925285.1_ASM1492528v1_genomic.fna.gz | prodigal -d GCF_014925285.1_ASM1492528v1_genomic.fna/cds.fna -a GCF_014925285.1_ASM1492528v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:10:45,980] [INFO] Task succeeded: Prodigal
[2024-01-25 18:10:45,980] [INFO] Task started: HMMsearch
[2024-01-25 18:10:45,981] [INFO] Running command: hmmsearch --tblout GCF_014925285.1_ASM1492528v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4409e99-3666-4292-8b8c-5f18b96d36c8/dqc_reference/reference_markers.hmm GCF_014925285.1_ASM1492528v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:10:46,242] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:10:46,244] [INFO] Found 6/6 markers.
[2024-01-25 18:10:46,280] [INFO] Query marker FASTA was written to GCF_014925285.1_ASM1492528v1_genomic.fna/markers.fasta
[2024-01-25 18:10:46,281] [INFO] Task started: Blastn
[2024-01-25 18:10:46,281] [INFO] Running command: blastn -query GCF_014925285.1_ASM1492528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4409e99-3666-4292-8b8c-5f18b96d36c8/dqc_reference/reference_markers.fasta -out GCF_014925285.1_ASM1492528v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:46,983] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:46,986] [INFO] Selected 11 target genomes.
[2024-01-25 18:10:46,986] [INFO] Target genome list was writen to GCF_014925285.1_ASM1492528v1_genomic.fna/target_genomes.txt
[2024-01-25 18:10:46,988] [INFO] Task started: fastANI
[2024-01-25 18:10:46,988] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd987bf3-9d3e-4e62-98e2-364af74c40a8/GCF_014925285.1_ASM1492528v1_genomic.fna.gz --refList GCF_014925285.1_ASM1492528v1_genomic.fna/target_genomes.txt --output GCF_014925285.1_ASM1492528v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:10:56,738] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:56,739] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4409e99-3666-4292-8b8c-5f18b96d36c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:10:56,739] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4409e99-3666-4292-8b8c-5f18b96d36c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:10:56,746] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:10:56,747] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:10:56,747] [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
Pseudoalteromonas lipolytica	strain=LMEB 39	GCA_014925285.1	570156	570156	suspected-type	True	100.0	1507	1508	95	conclusive
Pseudoalteromonas lipolytica	strain=CGMCC 1.8499	GCA_900116435.1	570156	570156	suspected-type	True	99.9667	1478	1508	95	conclusive
Pseudoalteromonas profundi	strain=CGMCC 1.15394	GCA_014642695.1	1774956	1774956	type	True	83.9563	1051	1508	95	below_threshold
Pseudoalteromonas shioyasakiensis	strain=JCM 18891	GCA_001550135.1	1190813	1190813	suspected-type	True	83.9003	1052	1508	95	below_threshold
Pseudoalteromonas gelatinilytica	strain=NH153	GCA_001641615.1	1703256	1703256	type	True	83.8217	1070	1508	95	below_threshold
Pseudoalteromonas arabiensis	strain=JCM 17292	GCA_001550155.1	874454	874454	type	True	83.2084	983	1508	95	below_threshold
Psychrosphaera ytuae	strain=MTZ26	GCA_017638545.1	2820710	2820710	type	True	79.7343	85	1508	95	below_threshold
Vibrio algicola	strain=SM1977	GCA_009601765.2	2662262	2662262	type	True	76.4698	56	1508	95	below_threshold
Shewanella sairae	strain=LMG 21408	GCA_023283535.1	190310	190310	type	True	76.4243	60	1508	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	75.9731	75	1508	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	75.8673	74	1508	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:10:56,748] [INFO] DFAST Taxonomy check result was written to GCF_014925285.1_ASM1492528v1_genomic.fna/tc_result.tsv
[2024-01-25 18:10:56,749] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:10:56,749] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:10:56,749] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4409e99-3666-4292-8b8c-5f18b96d36c8/dqc_reference/checkm_data
[2024-01-25 18:10:56,750] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:10:56,791] [INFO] Task started: CheckM
[2024-01-25 18:10:56,791] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014925285.1_ASM1492528v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014925285.1_ASM1492528v1_genomic.fna/checkm_input GCF_014925285.1_ASM1492528v1_genomic.fna/checkm_result
[2024-01-25 18:11:26,901] [INFO] Task succeeded: CheckM
[2024-01-25 18:11:26,902] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:11:26,927] [INFO] ===== Completeness check finished =====
[2024-01-25 18:11:26,927] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:11:26,927] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014925285.1_ASM1492528v1_genomic.fna/markers.fasta)
[2024-01-25 18:11:26,928] [INFO] Task started: Blastn
[2024-01-25 18:11:26,928] [INFO] Running command: blastn -query GCF_014925285.1_ASM1492528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4409e99-3666-4292-8b8c-5f18b96d36c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_014925285.1_ASM1492528v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:28,010] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:28,013] [INFO] Selected 11 target genomes.
[2024-01-25 18:11:28,014] [INFO] Target genome list was writen to GCF_014925285.1_ASM1492528v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:11:28,015] [INFO] Task started: fastANI
[2024-01-25 18:11:28,015] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd987bf3-9d3e-4e62-98e2-364af74c40a8/GCF_014925285.1_ASM1492528v1_genomic.fna.gz --refList GCF_014925285.1_ASM1492528v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014925285.1_ASM1492528v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:11:38,512] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:38,520] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:11:38,520] [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_900116435.1	s__Pseudoalteromonas lipolytica	99.9667	1478	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.07	98.83	0.92	0.86	12	conclusive
GCA_002684115.1	s__Pseudoalteromonas sp002684115	85.5797	225	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	97.0029	97.90	97.71	0.79	0.79	5	-
GCF_013391845.1	s__Pseudoalteromonas sp002685175	84.0123	873	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.05	98.96	0.91	0.83	5	-
GCF_001550135.1	s__Pseudoalteromonas shioyasakiensis	83.9108	1050	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	97.0029	98.58	98.56	0.94	0.92	4	-
GCF_004792295.1	s__Pseudoalteromonas lipolytica_C	83.9073	1008	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.42	98.24	0.87	0.68	9	-
GCF_001641615.1	s__Pseudoalteromonas gelatinilytica	83.8234	1070	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.27	97.45	0.92	0.88	6	-
GCF_013349995.1	s__Pseudoalteromonas sp013349995	83.7674	1014	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.6093	97.46	97.37	0.85	0.84	6	-
GCF_001469895.1	s__Pseudoalteromonas sp001469895	83.7199	1029	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	96.7314	N/A	N/A	N/A	N/A	1	-
GCF_019134595.1	s__Pseudoalteromonas shioyasakiensis_A	83.6537	1050	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.6918	N/A	N/A	N/A	N/A	1	-
GCF_001306915.1	s__Pseudoalteromonas lipolytica_A	83.5702	1003	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.22	97.66	0.91	0.90	9	-
GCF_001550155.1	s__Pseudoalteromonas arabiensis	83.1998	984	1508	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.77	95.60	0.91	0.90	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:11:38,525] [INFO] GTDB search result was written to GCF_014925285.1_ASM1492528v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:11:38,525] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:11:38,531] [INFO] DFAST_QC result json was written to GCF_014925285.1_ASM1492528v1_genomic.fna/dqc_result.json
[2024-01-25 18:11:38,531] [INFO] DFAST_QC completed!
[2024-01-25 18:11:38,531] [INFO] Total running time: 0h1m3s