[2024-01-24 13:46:25,394] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:25,395] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:25,395] [INFO] DQC Reference Directory: /var/lib/cwl/stg8942f7d1-c0af-433b-b8c4-6756b7b437a2/dqc_reference
[2024-01-24 13:46:26,735] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:26,735] [INFO] Task started: Prodigal
[2024-01-24 13:46:26,736] [INFO] Running command: gunzip -c /var/lib/cwl/stge423d2b9-3ab6-48d0-8688-e0b415966c73/GCF_000015285.1_ASM1528v1_genomic.fna.gz | prodigal -d GCF_000015285.1_ASM1528v1_genomic.fna/cds.fna -a GCF_000015285.1_ASM1528v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:36,583] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:36,583] [INFO] Task started: HMMsearch
[2024-01-24 13:46:36,583] [INFO] Running command: hmmsearch --tblout GCF_000015285.1_ASM1528v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8942f7d1-c0af-433b-b8c4-6756b7b437a2/dqc_reference/reference_markers.hmm GCF_000015285.1_ASM1528v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:36,860] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:36,861] [INFO] Found 6/6 markers.
[2024-01-24 13:46:36,897] [INFO] Query marker FASTA was written to GCF_000015285.1_ASM1528v1_genomic.fna/markers.fasta
[2024-01-24 13:46:36,898] [INFO] Task started: Blastn
[2024-01-24 13:46:36,898] [INFO] Running command: blastn -query GCF_000015285.1_ASM1528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8942f7d1-c0af-433b-b8c4-6756b7b437a2/dqc_reference/reference_markers.fasta -out GCF_000015285.1_ASM1528v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:37,613] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:37,616] [INFO] Selected 18 target genomes.
[2024-01-24 13:46:37,616] [INFO] Target genome list was writen to GCF_000015285.1_ASM1528v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:37,638] [INFO] Task started: fastANI
[2024-01-24 13:46:37,638] [INFO] Running command: fastANI --query /var/lib/cwl/stge423d2b9-3ab6-48d0-8688-e0b415966c73/GCF_000015285.1_ASM1528v1_genomic.fna.gz --refList GCF_000015285.1_ASM1528v1_genomic.fna/target_genomes.txt --output GCF_000015285.1_ASM1528v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:53,060] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:53,061] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8942f7d1-c0af-433b-b8c4-6756b7b437a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:53,061] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8942f7d1-c0af-433b-b8c4-6756b7b437a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:53,078] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:53,079] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:53,079] [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
Psychromonas ingrahamii	strain=37	GCA_000015285.1	357794	357794	type	True	100.0	1519	1519	95	conclusive
Psychromonas antarctica	strain=DSM 10704	GCA_022267535.1	67573	67573	type	True	78.4557	296	1519	95	below_threshold
Psychromonas ossibalaenae	strain=JAMM 0738	GCA_000381745.1	444922	444922	type	True	78.3902	321	1519	95	below_threshold
Psychromonas aquimarina	strain=ATCC BAA-1526	GCA_000428725.1	444919	444919	type	True	78.2294	319	1519	95	below_threshold
Psychromonas arctica	strain=DSM 14288	GCA_000482725.1	168275	168275	type	True	78.1017	237	1519	95	below_threshold
Psychromonas hadalis	strain=ATCC BAA-638	GCA_000420245.1	211669	211669	type	True	77.7126	224	1519	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	77.1103	56	1519	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:53,085] [INFO] DFAST Taxonomy check result was written to GCF_000015285.1_ASM1528v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:53,088] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:53,088] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:53,089] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8942f7d1-c0af-433b-b8c4-6756b7b437a2/dqc_reference/checkm_data
[2024-01-24 13:46:53,090] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:53,144] [INFO] Task started: CheckM
[2024-01-24 13:46:53,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000015285.1_ASM1528v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000015285.1_ASM1528v1_genomic.fna/checkm_input GCF_000015285.1_ASM1528v1_genomic.fna/checkm_result
[2024-01-24 13:47:27,821] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:27,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:27,843] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:27,843] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:27,843] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000015285.1_ASM1528v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:27,844] [INFO] Task started: Blastn
[2024-01-24 13:47:27,844] [INFO] Running command: blastn -query GCF_000015285.1_ASM1528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8942f7d1-c0af-433b-b8c4-6756b7b437a2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000015285.1_ASM1528v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:28,925] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:28,929] [INFO] Selected 8 target genomes.
[2024-01-24 13:47:28,929] [INFO] Target genome list was writen to GCF_000015285.1_ASM1528v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:28,943] [INFO] Task started: fastANI
[2024-01-24 13:47:28,944] [INFO] Running command: fastANI --query /var/lib/cwl/stge423d2b9-3ab6-48d0-8688-e0b415966c73/GCF_000015285.1_ASM1528v1_genomic.fna.gz --refList GCF_000015285.1_ASM1528v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000015285.1_ASM1528v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:36,702] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:36,715] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:36,715] [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_000015285.1	s__Psychromonas ingrahamii	100.0	1519	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002836415.1	s__Psychromonas sp002836415	90.0207	1042	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013619145.1	s__Psychromonas sp013619145	78.3914	354	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381745.1	s__Psychromonas ossibalaenae	78.3452	321	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011378715.1	s__Psychromonas sp011378715	78.3407	243	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003318165.1	s__Psychromonas sp003318165	78.3298	168	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428725.1	s__Psychromonas aquimarina	78.225	318	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004376845.1	s__Psychromonas sp004376845	78.0348	192	1519	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:36,717] [INFO] GTDB search result was written to GCF_000015285.1_ASM1528v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:36,718] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:36,721] [INFO] DFAST_QC result json was written to GCF_000015285.1_ASM1528v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:36,722] [INFO] DFAST_QC completed!
[2024-01-24 13:47:36,722] [INFO] Total running time: 0h1m11s