[2024-01-24 13:49:13,392] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:13,393] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:13,393] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2afde75-d747-49c9-b84f-0550b25dddcc/dqc_reference
[2024-01-24 13:49:14,680] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:14,681] [INFO] Task started: Prodigal
[2024-01-24 13:49:14,682] [INFO] Running command: gunzip -c /var/lib/cwl/stgc68d617d-e62a-42ac-8d75-b7f58b6d57fa/GCF_003383595.3_ASM338359v3_genomic.fna.gz | prodigal -d GCF_003383595.3_ASM338359v3_genomic.fna/cds.fna -a GCF_003383595.3_ASM338359v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:15,822] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:15,822] [INFO] Task started: HMMsearch
[2024-01-24 13:49:15,822] [INFO] Running command: hmmsearch --tblout GCF_003383595.3_ASM338359v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2afde75-d747-49c9-b84f-0550b25dddcc/dqc_reference/reference_markers.hmm GCF_003383595.3_ASM338359v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:16,080] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:16,091] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgc68d617d-e62a-42ac-8d75-b7f58b6d57fa/GCF_003383595.3_ASM338359v3_genomic.fna.gz]
[2024-01-24 13:49:16,104] [INFO] Query marker FASTA was written to GCF_003383595.3_ASM338359v3_genomic.fna/markers.fasta
[2024-01-24 13:49:16,104] [INFO] Task started: Blastn
[2024-01-24 13:49:16,104] [INFO] Running command: blastn -query GCF_003383595.3_ASM338359v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2afde75-d747-49c9-b84f-0550b25dddcc/dqc_reference/reference_markers.fasta -out GCF_003383595.3_ASM338359v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:16,686] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:16,690] [INFO] Selected 15 target genomes.
[2024-01-24 13:49:16,690] [INFO] Target genome list was writen to GCF_003383595.3_ASM338359v3_genomic.fna/target_genomes.txt
[2024-01-24 13:49:16,722] [INFO] Task started: fastANI
[2024-01-24 13:49:16,723] [INFO] Running command: fastANI --query /var/lib/cwl/stgc68d617d-e62a-42ac-8d75-b7f58b6d57fa/GCF_003383595.3_ASM338359v3_genomic.fna.gz --refList GCF_003383595.3_ASM338359v3_genomic.fna/target_genomes.txt --output GCF_003383595.3_ASM338359v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:22,332] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:22,333] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2afde75-d747-49c9-b84f-0550b25dddcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:22,333] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2afde75-d747-49c9-b84f-0550b25dddcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:22,341] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:49:22,341] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:49:22,341] [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
Mycoplasma struthionis	strain=237IA	GCA_003855455.1	538220	538220	type	True	79.301	76	246	95	below_threshold
Metamycoplasma auris	strain=ATCC 51348	GCA_003253435.1	51363	51363	type	True	79.2301	77	246	95	below_threshold
Metamycoplasma alkalescens	strain=NCTC10135	GCA_900476125.1	45363	45363	type	True	78.8206	87	246	95	below_threshold
Metamycoplasma alkalescens	strain=ATCC 29103	GCA_003208575.1	45363	45363	type	True	78.41	89	246	95	below_threshold
Metamycoplasma falconis	strain=ATCC 51372	GCA_006385795.1	92403	92403	type	True	78.2438	62	246	95	below_threshold
Metamycoplasma orale	strain=NCTC10112	GCA_900660435.1	2121	2121	type	True	77.6375	55	246	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:22,343] [INFO] DFAST Taxonomy check result was written to GCF_003383595.3_ASM338359v3_genomic.fna/tc_result.tsv
[2024-01-24 13:49:22,348] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:22,349] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:22,349] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2afde75-d747-49c9-b84f-0550b25dddcc/dqc_reference/checkm_data
[2024-01-24 13:49:22,350] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:22,363] [INFO] Task started: CheckM
[2024-01-24 13:49:22,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003383595.3_ASM338359v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003383595.3_ASM338359v3_genomic.fna/checkm_input GCF_003383595.3_ASM338359v3_genomic.fna/checkm_result
[2024-01-24 13:49:34,491] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:34,492] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:34,507] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:34,507] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:34,508] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003383595.3_ASM338359v3_genomic.fna/markers.fasta)
[2024-01-24 13:49:34,508] [INFO] Task started: Blastn
[2024-01-24 13:49:34,508] [INFO] Running command: blastn -query GCF_003383595.3_ASM338359v3_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2afde75-d747-49c9-b84f-0550b25dddcc/dqc_reference/reference_markers_gtdb.fasta -out GCF_003383595.3_ASM338359v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:35,252] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:35,256] [INFO] Selected 18 target genomes.
[2024-01-24 13:49:35,256] [INFO] Target genome list was writen to GCF_003383595.3_ASM338359v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:35,267] [INFO] Task started: fastANI
[2024-01-24 13:49:35,267] [INFO] Running command: fastANI --query /var/lib/cwl/stgc68d617d-e62a-42ac-8d75-b7f58b6d57fa/GCF_003383595.3_ASM338359v3_genomic.fna.gz --refList GCF_003383595.3_ASM338359v3_genomic.fna/target_genomes_gtdb.txt --output GCF_003383595.3_ASM338359v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:39,827] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:39,841] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:39,841] [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_003383595.3	s__Metamycoplasma phocicerebrale	100.0	246	246	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017116825.1	s__Metamycoplasma enhydrae	80.9614	131	246	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900660725.1	s__Metamycoplasma arginini	79.9168	122	246	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	98.27	98.11	0.94	0.92	6	-
GCF_000828855.1	s__Metamycoplasma canadense	79.4641	121	246	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253435.1	s__Metamycoplasma auris	79.3525	75	246	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003855455.1	s__Metamycoplasma struthionis	79.2733	75	246	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	98.82	98.82	0.96	0.96	2	-
GCF_900476125.1	s__Metamycoplasma alkalescens	78.8104	89	246	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	99.14	98.30	0.97	0.94	3	-
GCF_000367765.1	s__Metamycoplasma auris_A	78.75	86	246	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000085865.1	s__Metamycoplasma hominis	78.5924	76	246	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	97.99	97.80	0.96	0.91	51	-
GCF_000702805.1	s__Metamycoplasma anseris	78.1788	67	246	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:39,843] [INFO] GTDB search result was written to GCF_003383595.3_ASM338359v3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:39,844] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:39,848] [INFO] DFAST_QC result json was written to GCF_003383595.3_ASM338359v3_genomic.fna/dqc_result.json
[2024-01-24 13:49:39,848] [INFO] DFAST_QC completed!
[2024-01-24 13:49:39,849] [INFO] Total running time: 0h0m26s