[2024-01-24 15:26:38,977] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:38,979] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:38,980] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d354975-11bd-48e6-a5aa-50a142696e92/dqc_reference
[2024-01-24 15:26:40,395] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:40,396] [INFO] Task started: Prodigal
[2024-01-24 15:26:40,397] [INFO] Running command: gunzip -c /var/lib/cwl/stgf87ec2cf-5bc6-4cac-903b-3d3e37546acb/GCF_007997385.1_ASM799738v1_genomic.fna.gz | prodigal -d GCF_007997385.1_ASM799738v1_genomic.fna/cds.fna -a GCF_007997385.1_ASM799738v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:51,944] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:51,944] [INFO] Task started: HMMsearch
[2024-01-24 15:26:51,944] [INFO] Running command: hmmsearch --tblout GCF_007997385.1_ASM799738v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d354975-11bd-48e6-a5aa-50a142696e92/dqc_reference/reference_markers.hmm GCF_007997385.1_ASM799738v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:52,259] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:52,261] [INFO] Found 6/6 markers.
[2024-01-24 15:26:52,296] [INFO] Query marker FASTA was written to GCF_007997385.1_ASM799738v1_genomic.fna/markers.fasta
[2024-01-24 15:26:52,296] [INFO] Task started: Blastn
[2024-01-24 15:26:52,296] [INFO] Running command: blastn -query GCF_007997385.1_ASM799738v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d354975-11bd-48e6-a5aa-50a142696e92/dqc_reference/reference_markers.fasta -out GCF_007997385.1_ASM799738v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:26:53,072] [INFO] Task succeeded: Blastn
[2024-01-24 15:26:53,077] [INFO] Selected 20 target genomes.
[2024-01-24 15:26:53,078] [INFO] Target genome list was writen to GCF_007997385.1_ASM799738v1_genomic.fna/target_genomes.txt
[2024-01-24 15:26:53,113] [INFO] Task started: fastANI
[2024-01-24 15:26:53,113] [INFO] Running command: fastANI --query /var/lib/cwl/stgf87ec2cf-5bc6-4cac-903b-3d3e37546acb/GCF_007997385.1_ASM799738v1_genomic.fna.gz --refList GCF_007997385.1_ASM799738v1_genomic.fna/target_genomes.txt --output GCF_007997385.1_ASM799738v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:07,947] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:07,948] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d354975-11bd-48e6-a5aa-50a142696e92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:07,948] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d354975-11bd-48e6-a5aa-50a142696e92/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:07,969] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:07,969] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:07,969] [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
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	100.0	1223	1225	95	conclusive
Seonamhaeicola marinus	strain=B011	GCA_008085455.1	1912246	1912246	type	True	80.0699	658	1225	95	below_threshold
Tamlana nanhaiensis	strain=FHC16	GCA_000943555.1	1382798	1382798	type	True	78.9008	477	1225	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	78.8455	532	1225	95	below_threshold
Seonamhaeicola aphaedonensis	strain=CECT 8487	GCA_003386195.1	1461338	1461338	type	True	78.8336	430	1225	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	78.7197	430	1225	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	78.2925	409	1225	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.2742	416	1225	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	78.2672	416	1225	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	78.2436	458	1225	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	78.1987	462	1225	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	78.1931	412	1225	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	78.0462	371	1225	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	78.0035	307	1225	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.8638	370	1225	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.8135	391	1225	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	77.712	389	1225	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.6608	326	1225	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	77.4887	274	1225	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	77.1782	223	1225	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:07,971] [INFO] DFAST Taxonomy check result was written to GCF_007997385.1_ASM799738v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:07,971] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:07,971] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:07,972] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d354975-11bd-48e6-a5aa-50a142696e92/dqc_reference/checkm_data
[2024-01-24 15:27:07,973] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:08,011] [INFO] Task started: CheckM
[2024-01-24 15:27:08,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007997385.1_ASM799738v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007997385.1_ASM799738v1_genomic.fna/checkm_input GCF_007997385.1_ASM799738v1_genomic.fna/checkm_result
[2024-01-24 15:27:44,173] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:44,174] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:44,196] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:44,197] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:44,197] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007997385.1_ASM799738v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:44,197] [INFO] Task started: Blastn
[2024-01-24 15:27:44,198] [INFO] Running command: blastn -query GCF_007997385.1_ASM799738v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d354975-11bd-48e6-a5aa-50a142696e92/dqc_reference/reference_markers_gtdb.fasta -out GCF_007997385.1_ASM799738v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:45,243] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:45,248] [INFO] Selected 16 target genomes.
[2024-01-24 15:27:45,249] [INFO] Target genome list was writen to GCF_007997385.1_ASM799738v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:45,262] [INFO] Task started: fastANI
[2024-01-24 15:27:45,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgf87ec2cf-5bc6-4cac-903b-3d3e37546acb/GCF_007997385.1_ASM799738v1_genomic.fna.gz --refList GCF_007997385.1_ASM799738v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007997385.1_ASM799738v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:57,070] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:57,083] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:57,084] [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_007997385.1	s__Seonamhaeicola algicola	100.0	1223	1225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001971785.1	s__Seonamhaeicola sp001971785	80.5558	619	1225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358095.2	s__Seonamhaeicola sp004358095	79.0022	495	1225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000943555.1	s__Tamlana_B nanhaiensis	78.9099	476	1225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008056315.1	s__Seonamhaeicola maritimus	78.8377	533	1225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003386195.1	s__Seonamhaeicola aphaedonensis	78.8252	431	1225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	78.7297	429	1225	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_900114265.1	s__Flaviramulus basaltis	78.6764	466	1225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	78.4238	446	1225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	78.2962	391	1225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141715.1	s__Arenitalea lutea	78.2742	416	1225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014202225.1	s__Algibacter_B amylolyticus	78.1984	462	1225	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_004791695.1	s__Flavivirga rizhaonensis	78.1931	412	1225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003425985.1	s__Mariniflexile sp002848895	78.0219	369	1225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000941055.1	s__Siansivirga zeaxanthinifaciens	77.986	373	1225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Siansivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860245.1	s__Tamlana_A agarivorans_A	77.9136	336	1225	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:57,085] [INFO] GTDB search result was written to GCF_007997385.1_ASM799738v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:57,086] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:57,090] [INFO] DFAST_QC result json was written to GCF_007997385.1_ASM799738v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:57,090] [INFO] DFAST_QC completed!
[2024-01-24 15:27:57,090] [INFO] Total running time: 0h1m18s