[2023-06-05 00:53:14,575] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:53:14,577] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:53:14,577] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c0fe303-afd6-4b3c-ae24-9d341136e49d/dqc_reference
[2023-06-05 00:53:15,945] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:53:15,946] [INFO] Task started: Prodigal
[2023-06-05 00:53:15,946] [INFO] Running command: gunzip -c /var/lib/cwl/stg42e5f737-4f8e-4bbb-8cf3-fc520dfb94be/GCA_001577575.1_ASM157757v1_genomic.fna.gz | prodigal -d GCA_001577575.1_ASM157757v1_genomic.fna/cds.fna -a GCA_001577575.1_ASM157757v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:53:28,887] [INFO] Task succeeded: Prodigal
[2023-06-05 00:53:28,887] [INFO] Task started: HMMsearch
[2023-06-05 00:53:28,887] [INFO] Running command: hmmsearch --tblout GCA_001577575.1_ASM157757v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c0fe303-afd6-4b3c-ae24-9d341136e49d/dqc_reference/reference_markers.hmm GCA_001577575.1_ASM157757v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:53:29,210] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:53:29,212] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg42e5f737-4f8e-4bbb-8cf3-fc520dfb94be/GCA_001577575.1_ASM157757v1_genomic.fna.gz]
[2023-06-05 00:53:29,263] [INFO] Query marker FASTA was written to GCA_001577575.1_ASM157757v1_genomic.fna/markers.fasta
[2023-06-05 00:53:29,264] [INFO] Task started: Blastn
[2023-06-05 00:53:29,264] [INFO] Running command: blastn -query GCA_001577575.1_ASM157757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c0fe303-afd6-4b3c-ae24-9d341136e49d/dqc_reference/reference_markers.fasta -out GCA_001577575.1_ASM157757v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:53:30,097] [INFO] Task succeeded: Blastn
[2023-06-05 00:53:30,102] [INFO] Selected 26 target genomes.
[2023-06-05 00:53:30,103] [INFO] Target genome list was writen to GCA_001577575.1_ASM157757v1_genomic.fna/target_genomes.txt
[2023-06-05 00:53:30,165] [INFO] Task started: fastANI
[2023-06-05 00:53:30,165] [INFO] Running command: fastANI --query /var/lib/cwl/stg42e5f737-4f8e-4bbb-8cf3-fc520dfb94be/GCA_001577575.1_ASM157757v1_genomic.fna.gz --refList GCA_001577575.1_ASM157757v1_genomic.fna/target_genomes.txt --output GCA_001577575.1_ASM157757v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:53:47,575] [INFO] Task succeeded: fastANI
[2023-06-05 00:53:47,575] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c0fe303-afd6-4b3c-ae24-9d341136e49d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:53:47,576] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c0fe303-afd6-4b3c-ae24-9d341136e49d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:53:47,597] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:53:47,597] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 00:53:47,597] [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 persicus	strain=IBRC-M 10445	GCA_900114155.1	930118	930118	type	True	84.0955	469	1069	95	below_threshold
Marinobacter persicus	strain=KCTC 23561	GCA_014652295.1	930118	930118	type	True	84.0152	471	1069	95	below_threshold
Marinobacter vinifirmus	strain=FB1	GCA_002258215.1	355591	355591	type	True	81.332	358	1069	95	below_threshold
Marinobacter oulmenensis	strain=DSM 22359	GCA_014201735.1	643747	643747	type	True	80.9385	371	1069	95	below_threshold
Marinobacter pelagius	strain=CGMCC 1.6775	GCA_900114925.1	379482	379482	type	True	80.5641	318	1069	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	80.4157	300	1069	95	below_threshold
Marinobacter shengliensis subsp. alexandrii	strain=LZ-6	GCA_005871095.1	2570350	1389223	type	True	80.4115	342	1069	95	below_threshold
Marinobacter shengliensis	strain=SL013A34A2	GCA_003007715.1	1389223	1389223	type	True	80.3701	335	1069	95	below_threshold
Marinobacter fuscus	strain=NH169-3	GCA_003007675.1	2109942	2109942	type	True	80.2276	298	1069	95	below_threshold
Marinobacter gudaonensis	strain=CGMCC 1.6294	GCA_900115175.1	375760	375760	type	True	80.1694	305	1069	95	below_threshold
Marinobacter lutaoensis	strain=T5054	GCA_001981305.1	135739	135739	type	True	79.8266	292	1069	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	79.7622	256	1069	95	below_threshold
Marinobacter santoriniensis	strain=NKSG1	GCA_000347775.1	523742	523742	type	True	79.7363	247	1069	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	79.645	270	1069	95	below_threshold
Marinobacter salinexigens	strain=ZYF650	GCA_008370345.1	2919747	2919747	type	True	79.6279	234	1069	95	below_threshold
Marinobacter sediminum	strain=R65	GCA_016820575.1	256323	256323	type	True	79.5981	277	1069	95	below_threshold
Marinobacter confluentis	strain=HJM-18	GCA_004785685.1	1697557	1697557	type	True	79.276	228	1069	95	below_threshold
Marinobacter confluentis	strain=KCTC 42705	GCA_008795935.1	1697557	1697557	type	True	79.2374	229	1069	95	below_threshold
Marinobacter mangrovi	strain=CHFG3-1-5	GCA_016798325.1	2803918	2803918	type	True	78.9762	230	1069	95	below_threshold
Marinobacter halotolerans	strain=NBRC 110910	GCA_008795985.1	1569211	1569211	type	True	78.9427	245	1069	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.4846	102	1069	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	77.3109	56	1069	95	below_threshold
Pseudomonas mangiferae	strain=DMKU BBB3-04	GCA_007109405.1	2593654	2593654	type	True	77.0847	90	1069	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	77.0608	79	1069	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	76.8661	66	1069	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.2683	51	1069	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 00:53:47,600] [INFO] DFAST Taxonomy check result was written to GCA_001577575.1_ASM157757v1_genomic.fna/tc_result.tsv
[2023-06-05 00:53:47,600] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:53:47,601] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:53:47,601] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c0fe303-afd6-4b3c-ae24-9d341136e49d/dqc_reference/checkm_data
[2023-06-05 00:53:47,602] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:53:47,650] [INFO] Task started: CheckM
[2023-06-05 00:53:47,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_001577575.1_ASM157757v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_001577575.1_ASM157757v1_genomic.fna/checkm_input GCA_001577575.1_ASM157757v1_genomic.fna/checkm_result
[2023-06-05 00:54:28,737] [INFO] Task succeeded: CheckM
[2023-06-05 00:54:28,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 18.63%
Strain heterogeneity: 71.43%
--------------------------------------------------------------------------------
[2023-06-05 00:54:28,766] [INFO] ===== Completeness check finished =====
[2023-06-05 00:54:28,767] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:54:28,767] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_001577575.1_ASM157757v1_genomic.fna/markers.fasta)
[2023-06-05 00:54:28,767] [INFO] Task started: Blastn
[2023-06-05 00:54:28,768] [INFO] Running command: blastn -query GCA_001577575.1_ASM157757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c0fe303-afd6-4b3c-ae24-9d341136e49d/dqc_reference/reference_markers_gtdb.fasta -out GCA_001577575.1_ASM157757v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:54:30,113] [INFO] Task succeeded: Blastn
[2023-06-05 00:54:30,119] [INFO] Selected 18 target genomes.
[2023-06-05 00:54:30,119] [INFO] Target genome list was writen to GCA_001577575.1_ASM157757v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:54:30,516] [INFO] Task started: fastANI
[2023-06-05 00:54:30,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg42e5f737-4f8e-4bbb-8cf3-fc520dfb94be/GCA_001577575.1_ASM157757v1_genomic.fna.gz --refList GCA_001577575.1_ASM157757v1_genomic.fna/target_genomes_gtdb.txt --output GCA_001577575.1_ASM157757v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:54:45,430] [INFO] Task succeeded: fastANI
[2023-06-05 00:54:45,449] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 00:54:45,449] [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_002934325.1	s__Marinobacter persicus_A	94.9901	641	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.99	99.99	0.99	0.99	3	-
GCF_900114155.1	s__Marinobacter persicus	84.0922	468	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.98	99.98	1.00	1.00	2	-
GCA_013393545.1	s__Marinobacter sp013393545	82.1802	405	1069	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	81.4413	339	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002258215.1	s__Marinobacter vinifirmus	81.3374	356	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	96.96	96.78	0.87	0.84	7	-
GCF_014201735.1	s__Marinobacter oulmenensis	80.9489	370	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114925.1	s__Marinobacter pelagius	80.5273	320	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650915.1	s__Marinobacter sp001650915	80.4935	322	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.33	97.47	0.91	0.86	4	-
GCF_900115175.1	s__Marinobacter gudaonensis	80.1506	306	1069	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	80.1468	277	1069	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	79.8118	247	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001981305.1	s__Marinobacter lutaoensis	79.8087	293	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	99.21	99.12	0.92	0.92	6	-
GCF_000166295.1	s__Marinobacter adhaerens	79.7372	283	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	96.6719	98.39	97.71	0.91	0.87	5	-
GCF_000347775.1	s__Marinobacter santoriniensis	79.7363	247	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820575.1	s__Marinobacter sediminum	79.5981	277	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258515.1	s__Marinobacter_A bohaiensis	79.4032	243	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter_A	95.0	98.52	98.52	0.96	0.96	2	-
GCF_004785685.1	s__Marinobacter confluentis	79.264	229	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008795985.1	s__Marinobacter halotolerans	78.9421	246	1069	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 00:54:45,451] [INFO] GTDB search result was written to GCA_001577575.1_ASM157757v1_genomic.fna/result_gtdb.tsv
[2023-06-05 00:54:45,452] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:54:45,460] [INFO] DFAST_QC result json was written to GCA_001577575.1_ASM157757v1_genomic.fna/dqc_result.json
[2023-06-05 00:54:45,461] [INFO] DFAST_QC completed!
[2023-06-05 00:54:45,461] [INFO] Total running time: 0h1m31s