[2024-01-24 12:22:18,532] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:18,534] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:18,534] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0852a16-b040-4f58-8ef7-867eb7a399f4/dqc_reference
[2024-01-24 12:22:19,862] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:19,863] [INFO] Task started: Prodigal
[2024-01-24 12:22:19,863] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb01bf17-e067-4145-ada5-2f89af30d8d1/GCF_000015045.1_ASM1504v1_genomic.fna.gz | prodigal -d GCF_000015045.1_ASM1504v1_genomic.fna/cds.fna -a GCF_000015045.1_ASM1504v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:33,093] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:33,093] [INFO] Task started: HMMsearch
[2024-01-24 12:22:33,093] [INFO] Running command: hmmsearch --tblout GCF_000015045.1_ASM1504v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0852a16-b040-4f58-8ef7-867eb7a399f4/dqc_reference/reference_markers.hmm GCF_000015045.1_ASM1504v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:33,407] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:33,408] [INFO] Found 6/6 markers.
[2024-01-24 12:22:33,445] [INFO] Query marker FASTA was written to GCF_000015045.1_ASM1504v1_genomic.fna/markers.fasta
[2024-01-24 12:22:33,445] [INFO] Task started: Blastn
[2024-01-24 12:22:33,445] [INFO] Running command: blastn -query GCF_000015045.1_ASM1504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0852a16-b040-4f58-8ef7-867eb7a399f4/dqc_reference/reference_markers.fasta -out GCF_000015045.1_ASM1504v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:34,204] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:34,207] [INFO] Selected 10 target genomes.
[2024-01-24 12:22:34,207] [INFO] Target genome list was writen to GCF_000015045.1_ASM1504v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:34,211] [INFO] Task started: fastANI
[2024-01-24 12:22:34,212] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb01bf17-e067-4145-ada5-2f89af30d8d1/GCF_000015045.1_ASM1504v1_genomic.fna.gz --refList GCF_000015045.1_ASM1504v1_genomic.fna/target_genomes.txt --output GCF_000015045.1_ASM1504v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:42,751] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:42,751] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0852a16-b040-4f58-8ef7-867eb7a399f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:42,752] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0852a16-b040-4f58-8ef7-867eb7a399f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:42,761] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:42,761] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:42,761] [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
Pelobacter propionicus	strain=DSM 2379	GCA_000015045.1	29543	29543	type	True	100.0	1405	1413	95	conclusive
Oryzomonas sagensis	strain=Red100	GCA_008802355.1	2603857	2603857	type	True	79.0762	383	1413	95	below_threshold
Oryzomonas rubra	strain=Red88	GCA_008369015.1	2509454	2509454	type	True	78.8027	382	1413	95	below_threshold
Oryzomonas japonica	strain=Red96	GCA_008802365.1	2603858	2603858	type	True	78.7572	381	1413	95	below_threshold
Geobacter argillaceus	strain=ATCC BAA-1139	GCA_007830735.1	345631	345631	type	True	77.8021	211	1413	95	below_threshold
Geomonas paludis	strain=Red736	GCA_014193585.1	2740185	2740185	type	True	77.7371	261	1413	95	below_threshold
Geomonas propionica	strain=Red259	GCA_016458235.1	2798582	2798582	type	True	77.5857	236	1413	95	below_threshold
Geomonas azotofigens	strain=Red51	GCA_018919395.1	2843196	2843196	type	True	77.3207	268	1413	95	below_threshold
Geobacter chapellei	strain=DSM 13688	GCA_018531195.1	44671	44671	type	True	76.9505	178	1413	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:42,763] [INFO] DFAST Taxonomy check result was written to GCF_000015045.1_ASM1504v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:42,764] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:42,764] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:42,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0852a16-b040-4f58-8ef7-867eb7a399f4/dqc_reference/checkm_data
[2024-01-24 12:22:42,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:42,813] [INFO] Task started: CheckM
[2024-01-24 12:22:42,813] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000015045.1_ASM1504v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000015045.1_ASM1504v1_genomic.fna/checkm_input GCF_000015045.1_ASM1504v1_genomic.fna/checkm_result
[2024-01-24 12:23:23,019] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:23,021] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.70%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:23,040] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:23,041] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:23,041] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000015045.1_ASM1504v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:23,042] [INFO] Task started: Blastn
[2024-01-24 12:23:23,042] [INFO] Running command: blastn -query GCF_000015045.1_ASM1504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0852a16-b040-4f58-8ef7-867eb7a399f4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000015045.1_ASM1504v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:24,214] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:24,218] [INFO] Selected 15 target genomes.
[2024-01-24 12:23:24,218] [INFO] Target genome list was writen to GCF_000015045.1_ASM1504v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:24,244] [INFO] Task started: fastANI
[2024-01-24 12:23:24,245] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb01bf17-e067-4145-ada5-2f89af30d8d1/GCF_000015045.1_ASM1504v1_genomic.fna.gz --refList GCF_000015045.1_ASM1504v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000015045.1_ASM1504v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:35,249] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:35,261] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:35,261] [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_000015045.1	s__Pseudopelobacter propionicus	100.0	1407	1413	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Pseudopelobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016182975.1	s__JACPFJ01 sp016182975	79.727	306	1413	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACPFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008330225.1	s__Oryzomonas sp008330225	79.6373	415	1413	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013377095.1	s__Pseudopelobacter sp013377095	79.414	528	1413	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Pseudopelobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008802355.1	s__Oryzomonas sagensis	79.1003	381	1413	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298925.1	s__Pelotalea sp002298925	78.9418	332	1413	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Pelotalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015688915.1	s__JACPFJ01 sp015688915	78.8591	303	1413	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACPFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016865365.1	s__Pelotalea sp012556225	78.7724	388	1413	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Pelotalea	95.0	99.99	99.99	1.00	1.00	2	-
GCF_008802365.1	s__Oryzomonas japonica	78.7527	382	1413	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Oryzomonas	95.0	96.07	96.07	0.87	0.87	2	-
GCA_016650295.1	s__CAIPTY01 sp016650295	78.2615	305	1413	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__CAIPTY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003574895.1	s__JACPFJ01 sp003574895	77.7427	289	1413	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACPFJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016458235.1	s__Geomonas propionica	77.6008	235	1413	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Geobacteraceae;g__Geomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002424705.1	s__Trichlorobacter sp002424705	77.3335	137	1413	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__Trichlorobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013349325.1	s__JACRCG01 sp013349325	76.6004	127	1413	d__Bacteria;p__Desulfobacterota;c__Desulfuromonadia;o__Geobacterales;f__Pseudopelobacteraceae;g__JACRCG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:35,266] [INFO] GTDB search result was written to GCF_000015045.1_ASM1504v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:35,266] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:35,272] [INFO] DFAST_QC result json was written to GCF_000015045.1_ASM1504v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:35,272] [INFO] DFAST_QC completed!
[2024-01-24 12:23:35,272] [INFO] Total running time: 0h1m17s