[2024-01-25 18:43:05,928] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:05,929] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:05,929] [INFO] DQC Reference Directory: /var/lib/cwl/stg8cf29269-a5d3-4dc0-82d0-ea540e4228ce/dqc_reference
[2024-01-25 18:43:07,072] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:07,072] [INFO] Task started: Prodigal
[2024-01-25 18:43:07,073] [INFO] Running command: gunzip -c /var/lib/cwl/stgf3711030-6417-44d5-a5db-bd67ef935b33/GCF_021764745.1_ASM2176474v1_genomic.fna.gz | prodigal -d GCF_021764745.1_ASM2176474v1_genomic.fna/cds.fna -a GCF_021764745.1_ASM2176474v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:43:17,121] [INFO] Task succeeded: Prodigal
[2024-01-25 18:43:17,121] [INFO] Task started: HMMsearch
[2024-01-25 18:43:17,121] [INFO] Running command: hmmsearch --tblout GCF_021764745.1_ASM2176474v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8cf29269-a5d3-4dc0-82d0-ea540e4228ce/dqc_reference/reference_markers.hmm GCF_021764745.1_ASM2176474v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:43:17,352] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:43:17,353] [INFO] Found 6/6 markers.
[2024-01-25 18:43:17,386] [INFO] Query marker FASTA was written to GCF_021764745.1_ASM2176474v1_genomic.fna/markers.fasta
[2024-01-25 18:43:17,386] [INFO] Task started: Blastn
[2024-01-25 18:43:17,386] [INFO] Running command: blastn -query GCF_021764745.1_ASM2176474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cf29269-a5d3-4dc0-82d0-ea540e4228ce/dqc_reference/reference_markers.fasta -out GCF_021764745.1_ASM2176474v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:18,053] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:18,055] [INFO] Selected 22 target genomes.
[2024-01-25 18:43:18,056] [INFO] Target genome list was writen to GCF_021764745.1_ASM2176474v1_genomic.fna/target_genomes.txt
[2024-01-25 18:43:18,075] [INFO] Task started: fastANI
[2024-01-25 18:43:18,075] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3711030-6417-44d5-a5db-bd67ef935b33/GCF_021764745.1_ASM2176474v1_genomic.fna.gz --refList GCF_021764745.1_ASM2176474v1_genomic.fna/target_genomes.txt --output GCF_021764745.1_ASM2176474v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:43:34,456] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:34,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8cf29269-a5d3-4dc0-82d0-ea540e4228ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:43:34,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8cf29269-a5d3-4dc0-82d0-ea540e4228ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:43:34,470] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:43:34,470] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:43:34,470] [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
Joostella atrarenae	strain=M1-2	GCA_021764745.1	679257	679257	type	True	100.0	1301	1306	95	conclusive
Joostella marina	strain=DSM 19592	GCA_000260115.1	453852	453852	type	True	80.8276	746	1306	95	below_threshold
Galbibacter marinus	strain=ck-I2-15	GCA_000300875.1	555500	555500	type	True	77.5169	192	1306	95	below_threshold
Robertkochia solimangrovi	strain=CL23	GCA_007279655.1	2213046	2213046	type	True	77.202	117	1306	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	76.8635	139	1306	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.8604	99	1306	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	76.7791	106	1306	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	76.7472	168	1306	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.708	122	1306	95	below_threshold
Kordia aestuariivivens	strain=YSTF-M3	GCA_014397005.1	2759037	2759037	type	True	76.5633	123	1306	95	below_threshold
Winogradskyella wichelsiae	strain=Z738	GCA_013403925.1	2697007	2697007	type	True	76.5622	141	1306	95	below_threshold
Pustulibacterium marinum	strain=CGMCC 1.12333	GCA_900116665.1	1224947	1224947	type	True	76.5538	133	1306	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	76.55	129	1306	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.5048	85	1306	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	76.5036	135	1306	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	76.4881	153	1306	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	76.4318	108	1306	95	below_threshold
Maribacter vaceletii	strain=DSM 25230	GCA_003634105.1	1206816	1206816	type	True	76.4274	183	1306	95	below_threshold
Formosa sediminum	strain=PS13	GCA_007197735.1	2594004	2594004	type	True	76.3684	146	1306	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.3505	120	1306	95	below_threshold
Cellulophaga baltica	strain=DSM 24729	GCA_900102165.1	76594	76594	type	True	76.3433	149	1306	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	76.2572	145	1306	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:43:34,472] [INFO] DFAST Taxonomy check result was written to GCF_021764745.1_ASM2176474v1_genomic.fna/tc_result.tsv
[2024-01-25 18:43:34,472] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:43:34,473] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:43:34,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8cf29269-a5d3-4dc0-82d0-ea540e4228ce/dqc_reference/checkm_data
[2024-01-25 18:43:34,474] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:43:34,514] [INFO] Task started: CheckM
[2024-01-25 18:43:34,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021764745.1_ASM2176474v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021764745.1_ASM2176474v1_genomic.fna/checkm_input GCF_021764745.1_ASM2176474v1_genomic.fna/checkm_result
[2024-01-25 18:44:05,897] [INFO] Task succeeded: CheckM
[2024-01-25 18:44:05,898] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:44:05,922] [INFO] ===== Completeness check finished =====
[2024-01-25 18:44:05,922] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:44:05,923] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021764745.1_ASM2176474v1_genomic.fna/markers.fasta)
[2024-01-25 18:44:05,923] [INFO] Task started: Blastn
[2024-01-25 18:44:05,923] [INFO] Running command: blastn -query GCF_021764745.1_ASM2176474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8cf29269-a5d3-4dc0-82d0-ea540e4228ce/dqc_reference/reference_markers_gtdb.fasta -out GCF_021764745.1_ASM2176474v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:06,914] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:06,919] [INFO] Selected 19 target genomes.
[2024-01-25 18:44:06,920] [INFO] Target genome list was writen to GCF_021764745.1_ASM2176474v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:44:06,931] [INFO] Task started: fastANI
[2024-01-25 18:44:06,931] [INFO] Running command: fastANI --query /var/lib/cwl/stgf3711030-6417-44d5-a5db-bd67ef935b33/GCF_021764745.1_ASM2176474v1_genomic.fna.gz --refList GCF_021764745.1_ASM2176474v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021764745.1_ASM2176474v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:44:19,238] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:19,250] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 18:44:19,250] [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_000260115.1	s__Joostella marina	80.8224	747	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Joostella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391805.1	s__Galbibacter_A sp013391805	78.9985	410	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016734785.1	s__Galbibacter_A mesophilus	78.6329	413	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000300875.1	s__Galbibacter_B marinus	77.5169	192	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Galbibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007279655.1	s__Robertkochia solimangrovi	77.202	117	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Robertkochia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337215.1	s__Oceanihabitans sediminis	76.8635	139	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009797025.1	s__Cellulophaga sp009797025	76.8454	149	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386165.1	s__Winogradskyella eximia	76.6035	140	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016864015.1	s__Oceanihabitans sp016864015	76.5928	145	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003663945.1	s__Lacinutrix venerupis	76.5541	151	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	98.08	98.08	0.92	0.92	2	-
GCF_000797465.1	s__Psychroserpens jangbogonensis	76.55	129	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403925.1	s__Winogradskyella wichelsiae	76.5482	142	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860825.1	s__Oceanihabitans sp018860825	76.5412	167	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067265.1	s__Oceanihabitans sp018067265	76.4768	112	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202195.1	s__Oceanihabitans iliipiscarium	76.4727	125	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	76.4318	108	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634105.1	s__Maribacter_B vaceletii	76.4274	183	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102165.1	s__Cellulophaga baltica	76.3575	150	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	97.62	97.40	0.90	0.89	7	-
GCF_001418015.1	s__Lacinutrix mariniflava	76.2572	145	1306	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:44:19,252] [INFO] GTDB search result was written to GCF_021764745.1_ASM2176474v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:44:19,253] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:44:19,257] [INFO] DFAST_QC result json was written to GCF_021764745.1_ASM2176474v1_genomic.fna/dqc_result.json
[2024-01-25 18:44:19,257] [INFO] DFAST_QC completed!
[2024-01-25 18:44:19,257] [INFO] Total running time: 0h1m13s