[2023-07-01 02:28:15,931] [INFO] DFAST_QC pipeline started.
[2023-07-01 02:28:15,948] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 02:28:15,948] [INFO] DQC Reference Directory: /var/lib/cwl/stg67b482a1-a501-4bf8-9759-6472c43aa4a4/dqc_reference
[2023-07-01 02:28:18,241] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 02:28:18,241] [INFO] Task started: Prodigal
[2023-07-01 02:28:18,242] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b0e7e73-74f4-4edc-a3a9-eb8b8f1c8f31/GCA_007124535.1_ASM712453v1_genomic.fna.gz | prodigal -d GCA_007124535.1_ASM712453v1_genomic.fna/cds.fna -a GCA_007124535.1_ASM712453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 02:28:28,921] [INFO] Task succeeded: Prodigal
[2023-07-01 02:28:28,921] [INFO] Task started: HMMsearch
[2023-07-01 02:28:28,921] [INFO] Running command: hmmsearch --tblout GCA_007124535.1_ASM712453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67b482a1-a501-4bf8-9759-6472c43aa4a4/dqc_reference/reference_markers.hmm GCA_007124535.1_ASM712453v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 02:28:29,145] [INFO] Task succeeded: HMMsearch
[2023-07-01 02:28:29,147] [INFO] Found 6/6 markers.
[2023-07-01 02:28:29,180] [INFO] Query marker FASTA was written to GCA_007124535.1_ASM712453v1_genomic.fna/markers.fasta
[2023-07-01 02:28:29,180] [INFO] Task started: Blastn
[2023-07-01 02:28:29,181] [INFO] Running command: blastn -query GCA_007124535.1_ASM712453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67b482a1-a501-4bf8-9759-6472c43aa4a4/dqc_reference/reference_markers.fasta -out GCA_007124535.1_ASM712453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:28:29,751] [INFO] Task succeeded: Blastn
[2023-07-01 02:28:29,755] [INFO] Selected 20 target genomes.
[2023-07-01 02:28:29,756] [INFO] Target genome list was writen to GCA_007124535.1_ASM712453v1_genomic.fna/target_genomes.txt
[2023-07-01 02:28:29,758] [INFO] Task started: fastANI
[2023-07-01 02:28:29,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b0e7e73-74f4-4edc-a3a9-eb8b8f1c8f31/GCA_007124535.1_ASM712453v1_genomic.fna.gz --refList GCA_007124535.1_ASM712453v1_genomic.fna/target_genomes.txt --output GCA_007124535.1_ASM712453v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 02:28:51,549] [INFO] Task succeeded: fastANI
[2023-07-01 02:28:51,549] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67b482a1-a501-4bf8-9759-6472c43aa4a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 02:28:51,549] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67b482a1-a501-4bf8-9759-6472c43aa4a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 02:28:51,554] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 02:28:51,554] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 02:28:51,554] [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
Roseimaritima sediminicola	strain=JC651	GCA_009618275.1	2662066	2662066	type	True	75.5119	55	1080	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 02:28:51,556] [INFO] DFAST Taxonomy check result was written to GCA_007124535.1_ASM712453v1_genomic.fna/tc_result.tsv
[2023-07-01 02:28:51,557] [INFO] ===== Taxonomy check completed =====
[2023-07-01 02:28:51,557] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 02:28:51,558] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67b482a1-a501-4bf8-9759-6472c43aa4a4/dqc_reference/checkm_data
[2023-07-01 02:28:51,559] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 02:28:51,602] [INFO] Task started: CheckM
[2023-07-01 02:28:51,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_007124535.1_ASM712453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_007124535.1_ASM712453v1_genomic.fna/checkm_input GCA_007124535.1_ASM712453v1_genomic.fna/checkm_result
[2023-07-01 02:29:25,362] [INFO] Task succeeded: CheckM
[2023-07-01 02:29:25,363] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 02:29:25,383] [INFO] ===== Completeness check finished =====
[2023-07-01 02:29:25,383] [INFO] ===== Start GTDB Search =====
[2023-07-01 02:29:25,383] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_007124535.1_ASM712453v1_genomic.fna/markers.fasta)
[2023-07-01 02:29:25,383] [INFO] Task started: Blastn
[2023-07-01 02:29:25,384] [INFO] Running command: blastn -query GCA_007124535.1_ASM712453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67b482a1-a501-4bf8-9759-6472c43aa4a4/dqc_reference/reference_markers_gtdb.fasta -out GCA_007124535.1_ASM712453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 02:29:26,143] [INFO] Task succeeded: Blastn
[2023-07-01 02:29:26,146] [INFO] Selected 19 target genomes.
[2023-07-01 02:29:26,146] [INFO] Target genome list was writen to GCA_007124535.1_ASM712453v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 02:29:26,150] [INFO] Task started: fastANI
[2023-07-01 02:29:26,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b0e7e73-74f4-4edc-a3a9-eb8b8f1c8f31/GCA_007124535.1_ASM712453v1_genomic.fna.gz --refList GCA_007124535.1_ASM712453v1_genomic.fna/target_genomes_gtdb.txt --output GCA_007124535.1_ASM712453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 02:29:42,644] [INFO] Task succeeded: fastANI
[2023-07-01 02:29:42,652] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 02:29:42,653] [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
GCA_007124535.1	s__SLMF01 sp007124535	100.0	1066	1080	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__SLMF01	95.0	98.29	97.04	0.79	0.72	5	conclusive
GCA_007133715.1	s__SLMF01 sp007133715	81.6784	569	1080	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__SLMF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007121535.1	s__SKKK01 sp007121535	77.8881	210	1080	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__SKKK01	95.0	99.67	99.63	0.89	0.86	4	-
GCA_012515235.1	s__Anammoximicrobium sp012515235	76.0301	131	1080	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Anammoximicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012729315.1	s__JAAYDI01 sp012729315	75.845	57	1080	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__JAAYDI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016931995.1	s__JAFGDS01 sp016931995	75.601	52	1080	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAFGDS01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009618275.1	s__Roseimaritima sp009618275	75.5119	55	1080	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Roseimaritima	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008065135.1	s__Roseimaritima ulvae	75.3465	50	1080	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Pirellulaceae;g__Roseimaritima	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-07-01 02:29:42,655] [INFO] GTDB search result was written to GCA_007124535.1_ASM712453v1_genomic.fna/result_gtdb.tsv
[2023-07-01 02:29:42,655] [INFO] ===== GTDB Search completed =====
[2023-07-01 02:29:42,658] [INFO] DFAST_QC result json was written to GCA_007124535.1_ASM712453v1_genomic.fna/dqc_result.json
[2023-07-01 02:29:42,658] [INFO] DFAST_QC completed!
[2023-07-01 02:29:42,658] [INFO] Total running time: 0h1m27s