[2024-01-24 13:17:05,526] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:05,528] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:05,528] [INFO] DQC Reference Directory: /var/lib/cwl/stg80d4f1ad-46bb-46d0-bcad-b7c3a58c0e01/dqc_reference
[2024-01-24 13:17:06,885] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:06,886] [INFO] Task started: Prodigal
[2024-01-24 13:17:06,886] [INFO] Running command: gunzip -c /var/lib/cwl/stgadcd77de-4f4b-4812-a69e-63bf725b5991/GCF_024500045.1_ASM2450004v1_genomic.fna.gz | prodigal -d GCF_024500045.1_ASM2450004v1_genomic.fna/cds.fna -a GCF_024500045.1_ASM2450004v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:13,864] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:13,865] [INFO] Task started: HMMsearch
[2024-01-24 13:17:13,865] [INFO] Running command: hmmsearch --tblout GCF_024500045.1_ASM2450004v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg80d4f1ad-46bb-46d0-bcad-b7c3a58c0e01/dqc_reference/reference_markers.hmm GCF_024500045.1_ASM2450004v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:14,141] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:14,142] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgadcd77de-4f4b-4812-a69e-63bf725b5991/GCF_024500045.1_ASM2450004v1_genomic.fna.gz]
[2024-01-24 13:17:14,170] [INFO] Query marker FASTA was written to GCF_024500045.1_ASM2450004v1_genomic.fna/markers.fasta
[2024-01-24 13:17:14,170] [INFO] Task started: Blastn
[2024-01-24 13:17:14,171] [INFO] Running command: blastn -query GCF_024500045.1_ASM2450004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80d4f1ad-46bb-46d0-bcad-b7c3a58c0e01/dqc_reference/reference_markers.fasta -out GCF_024500045.1_ASM2450004v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:14,653] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:14,656] [INFO] Selected 9 target genomes.
[2024-01-24 13:17:14,656] [INFO] Target genome list was writen to GCF_024500045.1_ASM2450004v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:14,659] [INFO] Task started: fastANI
[2024-01-24 13:17:14,659] [INFO] Running command: fastANI --query /var/lib/cwl/stgadcd77de-4f4b-4812-a69e-63bf725b5991/GCF_024500045.1_ASM2450004v1_genomic.fna.gz --refList GCF_024500045.1_ASM2450004v1_genomic.fna/target_genomes.txt --output GCF_024500045.1_ASM2450004v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:19,179] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:19,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg80d4f1ad-46bb-46d0-bcad-b7c3a58c0e01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:19,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg80d4f1ad-46bb-46d0-bcad-b7c3a58c0e01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:19,186] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:19,187] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:19,187] [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
Methanolobus chelungpuianus	strain=St545Mb	GCA_024500045.1	502115	502115	type	True	100.0	848	848	95	conclusive
Methanolobus profundi	strain=Mob M	GCA_900114835.1	487685	487685	type	True	77.1582	162	848	95	below_threshold
Methanococcoides methylutens	strain=DSM 2657	GCA_000765475.1	2226	2226	type	True	76.8915	53	848	95	below_threshold
Methanococcoides methylutens		GCA_900773915.1	2226	2226	type	True	76.8511	55	848	95	below_threshold
Methanococcoides orientis	strain=LMO-1	GCA_021184045.1	2822137	2822137	type	True	76.5538	64	848	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:19,188] [INFO] DFAST Taxonomy check result was written to GCF_024500045.1_ASM2450004v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:19,189] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:19,189] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:19,189] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg80d4f1ad-46bb-46d0-bcad-b7c3a58c0e01/dqc_reference/checkm_data
[2024-01-24 13:17:19,191] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:19,217] [INFO] Task started: CheckM
[2024-01-24 13:17:19,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024500045.1_ASM2450004v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024500045.1_ASM2450004v1_genomic.fna/checkm_input GCF_024500045.1_ASM2450004v1_genomic.fna/checkm_result
[2024-01-24 13:17:46,112] [INFO] Task succeeded: CheckM
[2024-01-24 13:17:46,113] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:17:46,134] [INFO] ===== Completeness check finished =====
[2024-01-24 13:17:46,134] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:17:46,135] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024500045.1_ASM2450004v1_genomic.fna/markers.fasta)
[2024-01-24 13:17:46,135] [INFO] Task started: Blastn
[2024-01-24 13:17:46,135] [INFO] Running command: blastn -query GCF_024500045.1_ASM2450004v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg80d4f1ad-46bb-46d0-bcad-b7c3a58c0e01/dqc_reference/reference_markers_gtdb.fasta -out GCF_024500045.1_ASM2450004v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:46,565] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:46,568] [INFO] Selected 8 target genomes.
[2024-01-24 13:17:46,568] [INFO] Target genome list was writen to GCF_024500045.1_ASM2450004v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:17:46,593] [INFO] Task started: fastANI
[2024-01-24 13:17:46,594] [INFO] Running command: fastANI --query /var/lib/cwl/stgadcd77de-4f4b-4812-a69e-63bf725b5991/GCF_024500045.1_ASM2450004v1_genomic.fna.gz --refList GCF_024500045.1_ASM2450004v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024500045.1_ASM2450004v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:17:50,670] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:50,683] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:17:50,683] [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_000306725.1	s__Methanolobus psychrophilus	80.9112	558	848	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002501695.1	s__Methanolobus sp002501695	80.7231	443	848	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278365.1	s__Methanolobus sp016278365	80.5881	526	848	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002508635.1	s__Methanolobus sp002508635	77.5328	147	848	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016932675.1	s__Methanolobus sp016932675	77.409	200	848	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114835.1	s__Methanolobus profundi	77.1582	162	848	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006546655.1	s__Methanolobus vulcani_A	76.8486	107	848	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:17:50,685] [INFO] GTDB search result was written to GCF_024500045.1_ASM2450004v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:17:50,685] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:17:50,688] [INFO] DFAST_QC result json was written to GCF_024500045.1_ASM2450004v1_genomic.fna/dqc_result.json
[2024-01-24 13:17:50,688] [INFO] DFAST_QC completed!
[2024-01-24 13:17:50,688] [INFO] Total running time: 0h0m45s