[2024-01-24 13:25:29,643] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:29,645] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:29,645] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f2fe7df-ec50-413d-bcd9-43d2f789bfe5/dqc_reference
[2024-01-24 13:25:30,989] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:30,990] [INFO] Task started: Prodigal
[2024-01-24 13:25:30,990] [INFO] Running command: gunzip -c /var/lib/cwl/stge59f14c9-2568-44ba-85c9-91af2360c002/GCF_001981305.1_ASM198130v1_genomic.fna.gz | prodigal -d GCF_001981305.1_ASM198130v1_genomic.fna/cds.fna -a GCF_001981305.1_ASM198130v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:43,109] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:43,110] [INFO] Task started: HMMsearch
[2024-01-24 13:25:43,110] [INFO] Running command: hmmsearch --tblout GCF_001981305.1_ASM198130v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f2fe7df-ec50-413d-bcd9-43d2f789bfe5/dqc_reference/reference_markers.hmm GCF_001981305.1_ASM198130v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:43,402] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:43,403] [INFO] Found 6/6 markers.
[2024-01-24 13:25:43,441] [INFO] Query marker FASTA was written to GCF_001981305.1_ASM198130v1_genomic.fna/markers.fasta
[2024-01-24 13:25:43,441] [INFO] Task started: Blastn
[2024-01-24 13:25:43,441] [INFO] Running command: blastn -query GCF_001981305.1_ASM198130v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f2fe7df-ec50-413d-bcd9-43d2f789bfe5/dqc_reference/reference_markers.fasta -out GCF_001981305.1_ASM198130v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:44,329] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:44,334] [INFO] Selected 20 target genomes.
[2024-01-24 13:25:44,334] [INFO] Target genome list was writen to GCF_001981305.1_ASM198130v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:44,341] [INFO] Task started: fastANI
[2024-01-24 13:25:44,341] [INFO] Running command: fastANI --query /var/lib/cwl/stge59f14c9-2568-44ba-85c9-91af2360c002/GCF_001981305.1_ASM198130v1_genomic.fna.gz --refList GCF_001981305.1_ASM198130v1_genomic.fna/target_genomes.txt --output GCF_001981305.1_ASM198130v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:59,931] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:59,932] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f2fe7df-ec50-413d-bcd9-43d2f789bfe5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:59,932] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f2fe7df-ec50-413d-bcd9-43d2f789bfe5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:59,957] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:25:59,957] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:59,957] [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
Marinobacter lutaoensis	strain=T5054	GCA_001981305.1	135739	135739	type	True	100.0	1262	1262	95	conclusive
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	80.7353	655	1262	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	79.9445	600	1262	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	79.6252	565	1262	95	below_threshold
Marinobacter santoriniensis	strain=NKSG1	GCA_000347775.1	523742	523742	type	True	79.6081	552	1262	95	below_threshold
Marinobacter oulmenensis	strain=DSM 22359	GCA_014201735.1	643747	643747	type	True	79.608	521	1262	95	below_threshold
Marinobacter persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	79.581	452	1262	95	below_threshold
Marinobacter persicus	strain=KCTC 23561	GCA_014652295.1	930118	930118	type	True	79.5757	452	1262	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	79.5653	556	1262	95	below_threshold
Marinobacter subterrani	strain=JG233	GCA_001045555.1	1658765	1658765	type	True	79.4771	587	1262	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	79.4082	563	1262	95	below_threshold
Marinobacter profundi	strain=PWS21	GCA_002744715.1	2666256	2666256	type	True	79.2844	554	1262	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	79.207	500	1262	95	below_threshold
Marinobacter xestospongiae	strain=JCM 17469	GCA_023156385.1	994319	994319	type	True	79.1037	543	1262	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	79.0557	521	1262	95	below_threshold
Marinobacter guineae	strain=M3B	GCA_002744735.1	432303	432303	type	True	79.0364	556	1262	95	below_threshold
Marinobacter halodurans	strain=YJ-S3-2	GCA_004327985.1	2528979	2528979	type	True	78.9973	477	1262	95	below_threshold
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	78.8501	447	1262	95	below_threshold
Marinobacter nitratireducens	strain=AK21	GCA_000708045.1	1137280	1137280	type	True	78.8478	462	1262	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	78.7273	500	1262	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:59,960] [INFO] DFAST Taxonomy check result was written to GCF_001981305.1_ASM198130v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:59,960] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:59,960] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:59,961] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f2fe7df-ec50-413d-bcd9-43d2f789bfe5/dqc_reference/checkm_data
[2024-01-24 13:25:59,962] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:00,003] [INFO] Task started: CheckM
[2024-01-24 13:26:00,004] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001981305.1_ASM198130v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001981305.1_ASM198130v1_genomic.fna/checkm_input GCF_001981305.1_ASM198130v1_genomic.fna/checkm_result
[2024-01-24 13:26:37,271] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:37,273] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:37,291] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:37,292] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:37,292] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001981305.1_ASM198130v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:37,292] [INFO] Task started: Blastn
[2024-01-24 13:26:37,293] [INFO] Running command: blastn -query GCF_001981305.1_ASM198130v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f2fe7df-ec50-413d-bcd9-43d2f789bfe5/dqc_reference/reference_markers_gtdb.fasta -out GCF_001981305.1_ASM198130v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:38,784] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:38,795] [INFO] Selected 12 target genomes.
[2024-01-24 13:26:38,796] [INFO] Target genome list was writen to GCF_001981305.1_ASM198130v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:38,806] [INFO] Task started: fastANI
[2024-01-24 13:26:38,807] [INFO] Running command: fastANI --query /var/lib/cwl/stge59f14c9-2568-44ba-85c9-91af2360c002/GCF_001981305.1_ASM198130v1_genomic.fna.gz --refList GCF_001981305.1_ASM198130v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001981305.1_ASM198130v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:48,139] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:48,153] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:48,154] [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_001981305.1	s__Marinobacter lutaoensis	100.0	1262	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.21	99.12	0.92	0.92	6	conclusive
GCF_900114925.1	s__Marinobacter pelagius	80.7415	653	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315345.1	s__Marinobacter pelagius_A	80.5677	644	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623515.1	s__Marinobacter sp018623515	80.4721	544	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762755.1	s__Marinobacter sp014762755	80.0932	483	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115175.1	s__Marinobacter gudaonensis	79.9334	602	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000347775.1	s__Marinobacter santoriniensis	79.6081	552	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934325.1	s__Marinobacter persicus_A	79.6013	451	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	0.99	0.99	3	-
GCF_002744715.1	s__Marinobacter profundi	79.2858	553	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.28	99.28	0.94	0.94	2	-
GCF_004327985.1	s__Marinobacter_A halodurans	78.9733	480	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000708045.1	s__Marinobacter nitratireducens	78.8428	463	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.86	98.83	0.90	0.89	3	-
GCF_003789045.1	s__Marinobacter_A sp003789045	78.7322	509	1262	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	97.70	97.70	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:48,156] [INFO] GTDB search result was written to GCF_001981305.1_ASM198130v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:48,157] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:48,162] [INFO] DFAST_QC result json was written to GCF_001981305.1_ASM198130v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:48,162] [INFO] DFAST_QC completed!
[2024-01-24 13:26:48,162] [INFO] Total running time: 0h1m19s