[2023-06-17 11:26:26,767] [INFO] DFAST_QC pipeline started.
[2023-06-17 11:26:26,769] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 11:26:26,769] [INFO] DQC Reference Directory: /var/lib/cwl/stg9bf8eced-e6f5-49b3-8b6b-6615d54b39b0/dqc_reference
[2023-06-17 11:26:27,954] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 11:26:27,955] [INFO] Task started: Prodigal
[2023-06-17 11:26:27,956] [INFO] Running command: gunzip -c /var/lib/cwl/stgd52af567-3c55-4cb8-a40b-bd508097ea51/GCA_003488265.1_ASM348826v1_genomic.fna.gz | prodigal -d GCA_003488265.1_ASM348826v1_genomic.fna/cds.fna -a GCA_003488265.1_ASM348826v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 11:26:44,088] [INFO] Task succeeded: Prodigal
[2023-06-17 11:26:44,089] [INFO] Task started: HMMsearch
[2023-06-17 11:26:44,089] [INFO] Running command: hmmsearch --tblout GCA_003488265.1_ASM348826v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9bf8eced-e6f5-49b3-8b6b-6615d54b39b0/dqc_reference/reference_markers.hmm GCA_003488265.1_ASM348826v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 11:26:44,380] [INFO] Task succeeded: HMMsearch
[2023-06-17 11:26:44,382] [INFO] Found 6/6 markers.
[2023-06-17 11:26:44,432] [INFO] Query marker FASTA was written to GCA_003488265.1_ASM348826v1_genomic.fna/markers.fasta
[2023-06-17 11:26:44,433] [INFO] Task started: Blastn
[2023-06-17 11:26:44,433] [INFO] Running command: blastn -query GCA_003488265.1_ASM348826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bf8eced-e6f5-49b3-8b6b-6615d54b39b0/dqc_reference/reference_markers.fasta -out GCA_003488265.1_ASM348826v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:26:45,023] [INFO] Task succeeded: Blastn
[2023-06-17 11:26:45,028] [INFO] Selected 25 target genomes.
[2023-06-17 11:26:45,028] [INFO] Target genome list was writen to GCA_003488265.1_ASM348826v1_genomic.fna/target_genomes.txt
[2023-06-17 11:26:45,040] [INFO] Task started: fastANI
[2023-06-17 11:26:45,040] [INFO] Running command: fastANI --query /var/lib/cwl/stgd52af567-3c55-4cb8-a40b-bd508097ea51/GCA_003488265.1_ASM348826v1_genomic.fna.gz --refList GCA_003488265.1_ASM348826v1_genomic.fna/target_genomes.txt --output GCA_003488265.1_ASM348826v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 11:27:07,929] [INFO] Task succeeded: fastANI
[2023-06-17 11:27:07,930] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9bf8eced-e6f5-49b3-8b6b-6615d54b39b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 11:27:07,930] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9bf8eced-e6f5-49b3-8b6b-6615d54b39b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 11:27:07,939] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 11:27:07,939] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 11:27:07,939] [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
Caulifigura coniformis	strain=Pan44	GCA_007745175.1	2527983	2527983	type	True	75.8908	53	1809	95	below_threshold
Fuerstiella marisgermanici	strain=NH11	GCA_001983935.1	1891926	1891926	type	True	75.701	83	1809	95	below_threshold
Planctomicrobium piriforme	strain=DSM 26348	GCA_900113665.1	1576369	1576369	type	True	75.5378	64	1809	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 11:27:07,942] [INFO] DFAST Taxonomy check result was written to GCA_003488265.1_ASM348826v1_genomic.fna/tc_result.tsv
[2023-06-17 11:27:07,942] [INFO] ===== Taxonomy check completed =====
[2023-06-17 11:27:07,942] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 11:27:07,942] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9bf8eced-e6f5-49b3-8b6b-6615d54b39b0/dqc_reference/checkm_data
[2023-06-17 11:27:07,943] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 11:27:08,001] [INFO] Task started: CheckM
[2023-06-17 11:27:08,001] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003488265.1_ASM348826v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003488265.1_ASM348826v1_genomic.fna/checkm_input GCA_003488265.1_ASM348826v1_genomic.fna/checkm_result
[2023-06-17 11:27:58,067] [INFO] Task succeeded: CheckM
[2023-06-17 11:27:58,069] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 2.08%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-17 11:27:58,095] [INFO] ===== Completeness check finished =====
[2023-06-17 11:27:58,096] [INFO] ===== Start GTDB Search =====
[2023-06-17 11:27:58,096] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003488265.1_ASM348826v1_genomic.fna/markers.fasta)
[2023-06-17 11:27:58,096] [INFO] Task started: Blastn
[2023-06-17 11:27:58,096] [INFO] Running command: blastn -query GCA_003488265.1_ASM348826v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9bf8eced-e6f5-49b3-8b6b-6615d54b39b0/dqc_reference/reference_markers_gtdb.fasta -out GCA_003488265.1_ASM348826v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 11:27:59,175] [INFO] Task succeeded: Blastn
[2023-06-17 11:27:59,180] [INFO] Selected 22 target genomes.
[2023-06-17 11:27:59,180] [INFO] Target genome list was writen to GCA_003488265.1_ASM348826v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 11:27:59,196] [INFO] Task started: fastANI
[2023-06-17 11:27:59,197] [INFO] Running command: fastANI --query /var/lib/cwl/stgd52af567-3c55-4cb8-a40b-bd508097ea51/GCA_003488265.1_ASM348826v1_genomic.fna.gz --refList GCA_003488265.1_ASM348826v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003488265.1_ASM348826v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 11:28:17,764] [INFO] Task succeeded: fastANI
[2023-06-17 11:28:17,784] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 11:28:17,784] [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_005791255.1	s__SXXK01 sp005791255	98.2559	1328	1809	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	98.10	98.10	0.89	0.89	2	conclusive
GCA_903896675.1	s__SXXK01 sp903896675	86.6036	1303	1809	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	99.51	99.43	0.86	0.84	7	-
GCA_903858815.1	s__SXXK01 sp903858815	79.4683	897	1809	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	99.79	99.79	0.88	0.88	2	-
GCA_016795145.1	s__SXXK01 sp016795145	76.7359	175	1809	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903924405.1	s__SXXK01 sp903924405	76.6345	290	1809	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	99.71	99.71	0.88	0.88	2	-
GCA_903871805.1	s__SXXK01 sp903871805	76.3415	237	1809	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	99.56	99.46	0.84	0.84	3	-
GCA_003670925.1	s__SXXK01 sp003670925	76.0606	83	1809	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018242525.1	s__Schlesneria sp018242525	75.5399	70	1809	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Schlesneria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125225.1	s__DSVQ01 sp016125225	75.5011	52	1809	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__DSVQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005809115.1	s__F1-80-MAGs062 sp005809115	75.3029	53	1809	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__F1-80-MAGs062	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 11:28:17,787] [INFO] GTDB search result was written to GCA_003488265.1_ASM348826v1_genomic.fna/result_gtdb.tsv
[2023-06-17 11:28:17,788] [INFO] ===== GTDB Search completed =====
[2023-06-17 11:28:17,791] [INFO] DFAST_QC result json was written to GCA_003488265.1_ASM348826v1_genomic.fna/dqc_result.json
[2023-06-17 11:28:17,792] [INFO] DFAST_QC completed!
[2023-06-17 11:28:17,792] [INFO] Total running time: 0h1m51s