[2024-01-25 20:21:35,498] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:21:35,499] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:21:35,500] [INFO] DQC Reference Directory: /var/lib/cwl/stg62c98c62-491e-4681-b4c5-ad6190552804/dqc_reference
[2024-01-25 20:21:36,628] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:21:36,629] [INFO] Task started: Prodigal
[2024-01-25 20:21:36,629] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e51027f-b200-4ada-a8ab-f78adc37c70e/GCF_024360925.2_ASM2436092v2_genomic.fna.gz | prodigal -d GCF_024360925.2_ASM2436092v2_genomic.fna/cds.fna -a GCF_024360925.2_ASM2436092v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:21:49,280] [INFO] Task succeeded: Prodigal
[2024-01-25 20:21:49,280] [INFO] Task started: HMMsearch
[2024-01-25 20:21:49,280] [INFO] Running command: hmmsearch --tblout GCF_024360925.2_ASM2436092v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62c98c62-491e-4681-b4c5-ad6190552804/dqc_reference/reference_markers.hmm GCF_024360925.2_ASM2436092v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:21:49,561] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:21:49,562] [INFO] Found 6/6 markers.
[2024-01-25 20:21:49,598] [INFO] Query marker FASTA was written to GCF_024360925.2_ASM2436092v2_genomic.fna/markers.fasta
[2024-01-25 20:21:49,599] [INFO] Task started: Blastn
[2024-01-25 20:21:49,599] [INFO] Running command: blastn -query GCF_024360925.2_ASM2436092v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg62c98c62-491e-4681-b4c5-ad6190552804/dqc_reference/reference_markers.fasta -out GCF_024360925.2_ASM2436092v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:50,315] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:50,318] [INFO] Selected 17 target genomes.
[2024-01-25 20:21:50,318] [INFO] Target genome list was writen to GCF_024360925.2_ASM2436092v2_genomic.fna/target_genomes.txt
[2024-01-25 20:21:50,330] [INFO] Task started: fastANI
[2024-01-25 20:21:50,330] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e51027f-b200-4ada-a8ab-f78adc37c70e/GCF_024360925.2_ASM2436092v2_genomic.fna.gz --refList GCF_024360925.2_ASM2436092v2_genomic.fna/target_genomes.txt --output GCF_024360925.2_ASM2436092v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:22:03,490] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:03,490] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62c98c62-491e-4681-b4c5-ad6190552804/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:22:03,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62c98c62-491e-4681-b4c5-ad6190552804/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:22:03,498] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:22:03,498] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:22:03,499] [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
Methylomonas koyamae	strain=JCM 16701	GCA_001312005.1	702114	702114	suspected-type	True	79.7711	460	1530	95	below_threshold
Methylomonas koyamae	strain=Fw12E-Y	GCA_019669905.1	702114	702114	suspected-type	True	79.7569	504	1530	95	below_threshold
Methylomonas denitrificans	strain=FJG1	GCA_000785705.2	1538553	1538553	type	True	79.5553	516	1530	95	below_threshold
Methylomonas albis	strain=EbA	GCA_014850955.1	1854563	1854563	type	True	78.9215	420	1530	95	below_threshold
Methylomonas rhizoryzae	strain=GJ1	GCA_008632455.1	2608981	2608981	type	True	78.7464	377	1530	95	below_threshold
Methylomicrobium lacus	strain=LW14	GCA_000527095.1	136992	136992	type	True	77.5601	248	1530	95	below_threshold
Methylomarinum vadi	strain=IT-4	GCA_000733935.1	438855	438855	type	True	77.2325	234	1530	95	below_threshold
Allochromatium vinosum	strain=DSM 180	GCA_000025485.1	1049	1049	type	True	76.8967	51	1530	95	below_threshold
Methylobacter tundripaludum	strain=SV96	GCA_000190755.3	173365	173365	type	True	76.7279	134	1530	95	below_threshold
Methylogaea oryzae	strain=E10	GCA_019669985.1	1295382	1295382	type	True	76.7055	135	1530	95	below_threshold
Pseudomonas panipatensis	strain=CCM 7469	GCA_900099785.1	428992	428992	type	True	75.3857	56	1530	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:22:03,500] [INFO] DFAST Taxonomy check result was written to GCF_024360925.2_ASM2436092v2_genomic.fna/tc_result.tsv
[2024-01-25 20:22:03,501] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:22:03,501] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:22:03,502] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62c98c62-491e-4681-b4c5-ad6190552804/dqc_reference/checkm_data
[2024-01-25 20:22:03,502] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:22:03,546] [INFO] Task started: CheckM
[2024-01-25 20:22:03,546] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024360925.2_ASM2436092v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024360925.2_ASM2436092v2_genomic.fna/checkm_input GCF_024360925.2_ASM2436092v2_genomic.fna/checkm_result
[2024-01-25 20:22:41,374] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:41,376] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:41,392] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:41,392] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:41,393] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024360925.2_ASM2436092v2_genomic.fna/markers.fasta)
[2024-01-25 20:22:41,393] [INFO] Task started: Blastn
[2024-01-25 20:22:41,393] [INFO] Running command: blastn -query GCF_024360925.2_ASM2436092v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg62c98c62-491e-4681-b4c5-ad6190552804/dqc_reference/reference_markers_gtdb.fasta -out GCF_024360925.2_ASM2436092v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:42,659] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:42,662] [INFO] Selected 11 target genomes.
[2024-01-25 20:22:42,662] [INFO] Target genome list was writen to GCF_024360925.2_ASM2436092v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:42,694] [INFO] Task started: fastANI
[2024-01-25 20:22:42,694] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e51027f-b200-4ada-a8ab-f78adc37c70e/GCF_024360925.2_ASM2436092v2_genomic.fna.gz --refList GCF_024360925.2_ASM2436092v2_genomic.fna/target_genomes_gtdb.txt --output GCF_024360925.2_ASM2436092v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:52,299] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:52,307] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:22:52,307] [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_015711015.1	s__Methylomonas sp015711015	81.0157	688	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001312005.1	s__Methylomonas koyamae	79.7589	462	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	96.46	95.49	0.87	0.86	5	-
GCA_018335995.1	s__Methylomonas sp018335995	79.5934	428	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001644025.1	s__Methylomonas koyamae_A	79.5344	461	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	97.40	97.36	0.85	0.85	3	-
GCF_000515215.1	s__Methylomonas sp000515215	79.4542	468	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	95.46	95.46	0.83	0.83	2	-
GCA_001644045.1	s__Methylomonas methanica	79.3626	504	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	99.99	99.99	1.00	0.99	3	-
GCF_000214665.1	s__Methylomonas methanica_B	79.1462	507	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006483455.1	s__Methylomonas koyamae_B	79.0416	443	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002928965.1	s__Methylomonas sp002928965	79.0032	427	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004299305.1	s__Methylobacter_A sp004299305	76.182	115	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016784875.1	s__Methylobacter_A sp016784875	76.1416	53	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:22:52,308] [INFO] GTDB search result was written to GCF_024360925.2_ASM2436092v2_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:52,309] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:52,312] [INFO] DFAST_QC result json was written to GCF_024360925.2_ASM2436092v2_genomic.fna/dqc_result.json
[2024-01-25 20:22:52,312] [INFO] DFAST_QC completed!
[2024-01-25 20:22:52,312] [INFO] Total running time: 0h1m17s