[2023-06-29 02:58:02,547] [INFO] DFAST_QC pipeline started.
[2023-06-29 02:58:02,550] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 02:58:02,550] [INFO] DQC Reference Directory: /var/lib/cwl/stg518bdc22-9b4e-4b80-a9a0-a2cff2996808/dqc_reference
[2023-06-29 02:58:04,906] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 02:58:04,907] [INFO] Task started: Prodigal
[2023-06-29 02:58:04,907] [INFO] Running command: gunzip -c /var/lib/cwl/stgbdb2689b-967f-48df-8a80-86def3d1572a/GCA_027016405.1_ASM2701640v1_genomic.fna.gz | prodigal -d GCA_027016405.1_ASM2701640v1_genomic.fna/cds.fna -a GCA_027016405.1_ASM2701640v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 02:58:27,452] [INFO] Task succeeded: Prodigal
[2023-06-29 02:58:27,453] [INFO] Task started: HMMsearch
[2023-06-29 02:58:27,453] [INFO] Running command: hmmsearch --tblout GCA_027016405.1_ASM2701640v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg518bdc22-9b4e-4b80-a9a0-a2cff2996808/dqc_reference/reference_markers.hmm GCA_027016405.1_ASM2701640v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 02:58:27,715] [INFO] Task succeeded: HMMsearch
[2023-06-29 02:58:27,716] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbdb2689b-967f-48df-8a80-86def3d1572a/GCA_027016405.1_ASM2701640v1_genomic.fna.gz]
[2023-06-29 02:58:27,749] [INFO] Query marker FASTA was written to GCA_027016405.1_ASM2701640v1_genomic.fna/markers.fasta
[2023-06-29 02:58:27,749] [INFO] Task started: Blastn
[2023-06-29 02:58:27,749] [INFO] Running command: blastn -query GCA_027016405.1_ASM2701640v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg518bdc22-9b4e-4b80-a9a0-a2cff2996808/dqc_reference/reference_markers.fasta -out GCA_027016405.1_ASM2701640v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:58:28,347] [INFO] Task succeeded: Blastn
[2023-06-29 02:58:28,351] [INFO] Selected 31 target genomes.
[2023-06-29 02:58:28,352] [INFO] Target genome list was writen to GCA_027016405.1_ASM2701640v1_genomic.fna/target_genomes.txt
[2023-06-29 02:58:28,363] [INFO] Task started: fastANI
[2023-06-29 02:58:28,363] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdb2689b-967f-48df-8a80-86def3d1572a/GCA_027016405.1_ASM2701640v1_genomic.fna.gz --refList GCA_027016405.1_ASM2701640v1_genomic.fna/target_genomes.txt --output GCA_027016405.1_ASM2701640v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 02:58:47,916] [INFO] Task succeeded: fastANI
[2023-06-29 02:58:47,917] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg518bdc22-9b4e-4b80-a9a0-a2cff2996808/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 02:58:47,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg518bdc22-9b4e-4b80-a9a0-a2cff2996808/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 02:58:47,924] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 02:58:47,924] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 02:58:47,924] [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
Litorilinea aerophila	strain=ATCC BAA-2444	GCA_006569185.2	1204385	1204385	type	True	76.4163	94	905	95	below_threshold
Myxococcus virescens	strain=NBRC 100334	GCA_007989405.1	83456	83456	type	True	74.724	58	905	95	below_threshold
Myxococcus virescens	strain=DSM 2260	GCA_900101905.1	83456	83456	type	True	74.7182	59	905	95	below_threshold
Myxococcus xanthus	strain=DSM 16526	GCA_900106535.1	34	34	type	True	74.6972	52	905	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 02:58:47,926] [INFO] DFAST Taxonomy check result was written to GCA_027016405.1_ASM2701640v1_genomic.fna/tc_result.tsv
[2023-06-29 02:58:47,927] [INFO] ===== Taxonomy check completed =====
[2023-06-29 02:58:47,927] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 02:58:47,928] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg518bdc22-9b4e-4b80-a9a0-a2cff2996808/dqc_reference/checkm_data
[2023-06-29 02:58:47,930] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 02:58:47,973] [INFO] Task started: CheckM
[2023-06-29 02:58:47,974] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027016405.1_ASM2701640v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027016405.1_ASM2701640v1_genomic.fna/checkm_input GCA_027016405.1_ASM2701640v1_genomic.fna/checkm_result
[2023-06-29 02:59:33,411] [INFO] Task succeeded: CheckM
[2023-06-29 02:59:33,413] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.04%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 02:59:33,439] [INFO] ===== Completeness check finished =====
[2023-06-29 02:59:33,440] [INFO] ===== Start GTDB Search =====
[2023-06-29 02:59:33,441] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027016405.1_ASM2701640v1_genomic.fna/markers.fasta)
[2023-06-29 02:59:33,442] [INFO] Task started: Blastn
[2023-06-29 02:59:33,442] [INFO] Running command: blastn -query GCA_027016405.1_ASM2701640v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg518bdc22-9b4e-4b80-a9a0-a2cff2996808/dqc_reference/reference_markers_gtdb.fasta -out GCA_027016405.1_ASM2701640v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 02:59:34,307] [INFO] Task succeeded: Blastn
[2023-06-29 02:59:34,311] [INFO] Selected 26 target genomes.
[2023-06-29 02:59:34,311] [INFO] Target genome list was writen to GCA_027016405.1_ASM2701640v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 02:59:34,353] [INFO] Task started: fastANI
[2023-06-29 02:59:34,354] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdb2689b-967f-48df-8a80-86def3d1572a/GCA_027016405.1_ASM2701640v1_genomic.fna.gz --refList GCA_027016405.1_ASM2701640v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027016405.1_ASM2701640v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 02:59:49,205] [INFO] Task succeeded: fastANI
[2023-06-29 02:59:49,220] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 02:59:49,220] [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_011192085.1	s__M2005 sp011192085	82.2822	354	905	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__J102;f__J102;g__M2005	95.0	99.27	98.93	0.82	0.77	3	-
GCA_011371305.1	s__M2005 sp011371305	81.86	340	905	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__J102;f__J102;g__M2005	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015493675.1	s__M2005 sp015493675	79.9503	341	905	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__J102;f__J102;g__M2005	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015485435.1	s__M2005 sp015485435	78.0323	181	905	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__J102;f__J102;g__M2005	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015494005.1	s__S144-5 sp015494005	76.9667	99	905	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__S144-5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011176555.1	s__DUEF01 sp011176555	76.8408	119	905	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__J102;f__J102;g__DUEF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151415.1	s__JAADII01 sp013151415	76.8308	149	905	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__J102;f__J102;g__JAADII01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360575.1	s__JABWBG01 sp013360575	76.771	156	905	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__J102;f__J102;g__JABWBG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006569185.1	s__Litorilinea aerophila	76.43	92	905	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Litorilinea	95.0	99.85	99.85	0.99	0.99	2	-
GCA_003694905.1	s__J102 sp003694905	76.3026	93	905	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__J102;f__J102;g__J102	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013153375.1	s__JAADEN01 sp013153375	75.6072	55	905	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__DRMV01;g__JAADEN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011334325.1	s__DTPP01 sp011334325	75.5629	50	905	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__DTPP01;f__DTPP01;g__DTPP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 02:59:49,222] [INFO] GTDB search result was written to GCA_027016405.1_ASM2701640v1_genomic.fna/result_gtdb.tsv
[2023-06-29 02:59:49,223] [INFO] ===== GTDB Search completed =====
[2023-06-29 02:59:49,226] [INFO] DFAST_QC result json was written to GCA_027016405.1_ASM2701640v1_genomic.fna/dqc_result.json
[2023-06-29 02:59:49,226] [INFO] DFAST_QC completed!
[2023-06-29 02:59:49,226] [INFO] Total running time: 0h1m47s