[2024-01-24 14:05:33,486] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:33,491] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:33,492] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b0ab26a-1d18-4f71-a4c2-13aad339210a/dqc_reference
[2024-01-24 14:05:34,980] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:34,980] [INFO] Task started: Prodigal
[2024-01-24 14:05:34,981] [INFO] Running command: gunzip -c /var/lib/cwl/stgfe5b3843-3f2c-41e2-8ac4-e3085e494145/GCF_008933165.1_ASM893316v1_genomic.fna.gz | prodigal -d GCF_008933165.1_ASM893316v1_genomic.fna/cds.fna -a GCF_008933165.1_ASM893316v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:52,377] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:52,378] [INFO] Task started: HMMsearch
[2024-01-24 14:05:52,378] [INFO] Running command: hmmsearch --tblout GCF_008933165.1_ASM893316v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b0ab26a-1d18-4f71-a4c2-13aad339210a/dqc_reference/reference_markers.hmm GCF_008933165.1_ASM893316v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:52,652] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:52,653] [INFO] Found 6/6 markers.
[2024-01-24 14:05:52,697] [INFO] Query marker FASTA was written to GCF_008933165.1_ASM893316v1_genomic.fna/markers.fasta
[2024-01-24 14:05:52,698] [INFO] Task started: Blastn
[2024-01-24 14:05:52,698] [INFO] Running command: blastn -query GCF_008933165.1_ASM893316v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b0ab26a-1d18-4f71-a4c2-13aad339210a/dqc_reference/reference_markers.fasta -out GCF_008933165.1_ASM893316v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:53,312] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:53,315] [INFO] Selected 17 target genomes.
[2024-01-24 14:05:53,315] [INFO] Target genome list was writen to GCF_008933165.1_ASM893316v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:53,334] [INFO] Task started: fastANI
[2024-01-24 14:05:53,334] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe5b3843-3f2c-41e2-8ac4-e3085e494145/GCF_008933165.1_ASM893316v1_genomic.fna.gz --refList GCF_008933165.1_ASM893316v1_genomic.fna/target_genomes.txt --output GCF_008933165.1_ASM893316v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:04,013] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:04,013] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b0ab26a-1d18-4f71-a4c2-13aad339210a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:04,014] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b0ab26a-1d18-4f71-a4c2-13aad339210a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:04,026] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:06:04,026] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:04,027] [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
Phaeocystidibacter marisrubri	strain=JCM 30614	GCA_008933165.1	1577780	1577780	type	True	100.0	1109	1110	95	conclusive
Phaeocystidibacter marisrubri	strain=CGMCC 1.14954	GCA_014640415.1	1577780	1577780	type	True	99.9998	1109	1110	95	conclusive
Phaeocystidibacter luteus	strain=LMG 25704	GCA_008933115.1	911197	911197	type	True	78.1206	179	1110	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:04,028] [INFO] DFAST Taxonomy check result was written to GCF_008933165.1_ASM893316v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:04,029] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:04,029] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:04,029] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b0ab26a-1d18-4f71-a4c2-13aad339210a/dqc_reference/checkm_data
[2024-01-24 14:06:04,030] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:04,062] [INFO] Task started: CheckM
[2024-01-24 14:06:04,063] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008933165.1_ASM893316v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008933165.1_ASM893316v1_genomic.fna/checkm_input GCF_008933165.1_ASM893316v1_genomic.fna/checkm_result
[2024-01-24 14:06:59,060] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:59,061] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:59,076] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:59,076] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:59,076] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008933165.1_ASM893316v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:59,077] [INFO] Task started: Blastn
[2024-01-24 14:06:59,077] [INFO] Running command: blastn -query GCF_008933165.1_ASM893316v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b0ab26a-1d18-4f71-a4c2-13aad339210a/dqc_reference/reference_markers_gtdb.fasta -out GCF_008933165.1_ASM893316v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:59,886] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:59,889] [INFO] Selected 24 target genomes.
[2024-01-24 14:06:59,889] [INFO] Target genome list was writen to GCF_008933165.1_ASM893316v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:59,908] [INFO] Task started: fastANI
[2024-01-24 14:06:59,909] [INFO] Running command: fastANI --query /var/lib/cwl/stgfe5b3843-3f2c-41e2-8ac4-e3085e494145/GCF_008933165.1_ASM893316v1_genomic.fna.gz --refList GCF_008933165.1_ASM893316v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008933165.1_ASM893316v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:13,648] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:13,652] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:13,653] [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
GCF_008933165.1	s__Phaeocystidibacter marisrubri	100.0	1110	1110	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Phaeocystidibacter	95.0	99.07	98.14	0.97	0.95	3	conclusive
GCF_008933115.1	s__Phaeocystidibacter luteus	78.1206	179	1110	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Phaeocystidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373425.1	s__Phaeocystidibacter sp013373425	77.2452	148	1110	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__Phaeocystidibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:13,654] [INFO] GTDB search result was written to GCF_008933165.1_ASM893316v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:13,655] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:13,657] [INFO] DFAST_QC result json was written to GCF_008933165.1_ASM893316v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:13,657] [INFO] DFAST_QC completed!
[2024-01-24 14:07:13,657] [INFO] Total running time: 0h1m40s