[2024-01-25 18:00:05,890] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:00:05,892] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:00:05,892] [INFO] DQC Reference Directory: /var/lib/cwl/stgb4b439ca-0ba3-47d6-8382-42443b548e13/dqc_reference
[2024-01-25 18:00:07,053] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:00:07,054] [INFO] Task started: Prodigal
[2024-01-25 18:00:07,054] [INFO] Running command: gunzip -c /var/lib/cwl/stg3f19163a-bb77-4d17-9a58-761ed998c88c/GCF_001312005.1_ASM131200v1_genomic.fna.gz | prodigal -d GCF_001312005.1_ASM131200v1_genomic.fna/cds.fna -a GCF_001312005.1_ASM131200v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:00:19,049] [INFO] Task succeeded: Prodigal
[2024-01-25 18:00:19,050] [INFO] Task started: HMMsearch
[2024-01-25 18:00:19,050] [INFO] Running command: hmmsearch --tblout GCF_001312005.1_ASM131200v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb4b439ca-0ba3-47d6-8382-42443b548e13/dqc_reference/reference_markers.hmm GCF_001312005.1_ASM131200v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:00:19,366] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:00:19,367] [INFO] Found 6/6 markers.
[2024-01-25 18:00:19,418] [INFO] Query marker FASTA was written to GCF_001312005.1_ASM131200v1_genomic.fna/markers.fasta
[2024-01-25 18:00:19,419] [INFO] Task started: Blastn
[2024-01-25 18:00:19,419] [INFO] Running command: blastn -query GCF_001312005.1_ASM131200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4b439ca-0ba3-47d6-8382-42443b548e13/dqc_reference/reference_markers.fasta -out GCF_001312005.1_ASM131200v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:20,130] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:20,135] [INFO] Selected 16 target genomes.
[2024-01-25 18:00:20,135] [INFO] Target genome list was writen to GCF_001312005.1_ASM131200v1_genomic.fna/target_genomes.txt
[2024-01-25 18:00:20,203] [INFO] Task started: fastANI
[2024-01-25 18:00:20,203] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f19163a-bb77-4d17-9a58-761ed998c88c/GCF_001312005.1_ASM131200v1_genomic.fna.gz --refList GCF_001312005.1_ASM131200v1_genomic.fna/target_genomes.txt --output GCF_001312005.1_ASM131200v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:00:33,988] [INFO] Task succeeded: fastANI
[2024-01-25 18:00:33,989] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb4b439ca-0ba3-47d6-8382-42443b548e13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:00:33,989] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb4b439ca-0ba3-47d6-8382-42443b548e13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:00:33,997] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:00:33,998] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:00:33,998] [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	100.0	1450	1465	95	conclusive
Methylomonas koyamae	strain=Fw12E-Y	GCA_019669905.1	702114	702114	suspected-type	True	99.92	1463	1465	95	conclusive
Methylomonas denitrificans	strain=FJG1	GCA_000785705.2	1538553	1538553	type	True	80.0001	694	1465	95	below_threshold
Methylomonas albis	strain=EbA	GCA_014850955.1	1854563	1854563	type	True	79.4726	592	1465	95	below_threshold
Methylomonas rhizoryzae	strain=GJ1	GCA_008632455.1	2608981	2608981	type	True	79.2205	375	1465	95	below_threshold
Methylomarinum vadi	strain=IT-4	GCA_000733935.1	438855	438855	type	True	77.0887	212	1465	95	below_threshold
Methylomicrobium lacus	strain=LW14	GCA_000527095.1	136992	136992	type	True	77.0107	223	1465	95	below_threshold
Methylotuvimicrobium alcaliphilum	strain=20Z	GCA_000968535.1	271065	271065	type	True	76.6003	113	1465	95	below_threshold
Methylococcus geothermalis	strain=IM1	GCA_012769535.1	2681310	2681310	type	True	76.4664	111	1465	95	below_threshold
Methylobacter tundripaludum	strain=SV96	GCA_000190755.3	173365	173365	type	True	76.3342	144	1465	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	76.0464	63	1465	95	below_threshold
Pseudomonas capeferrum	strain=WCS358	GCA_022548835.1	1495066	1495066	type	True	75.5307	60	1465	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	75.4375	56	1465	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:00:33,999] [INFO] DFAST Taxonomy check result was written to GCF_001312005.1_ASM131200v1_genomic.fna/tc_result.tsv
[2024-01-25 18:00:33,999] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:00:33,999] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:00:33,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb4b439ca-0ba3-47d6-8382-42443b548e13/dqc_reference/checkm_data
[2024-01-25 18:00:34,000] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:00:34,048] [INFO] Task started: CheckM
[2024-01-25 18:00:34,048] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001312005.1_ASM131200v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001312005.1_ASM131200v1_genomic.fna/checkm_input GCF_001312005.1_ASM131200v1_genomic.fna/checkm_result
[2024-01-25 18:01:09,368] [INFO] Task succeeded: CheckM
[2024-01-25 18:01:09,369] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.25%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:01:09,387] [INFO] ===== Completeness check finished =====
[2024-01-25 18:01:09,387] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:01:09,388] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001312005.1_ASM131200v1_genomic.fna/markers.fasta)
[2024-01-25 18:01:09,388] [INFO] Task started: Blastn
[2024-01-25 18:01:09,388] [INFO] Running command: blastn -query GCF_001312005.1_ASM131200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb4b439ca-0ba3-47d6-8382-42443b548e13/dqc_reference/reference_markers_gtdb.fasta -out GCF_001312005.1_ASM131200v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:10,548] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:10,550] [INFO] Selected 17 target genomes.
[2024-01-25 18:01:10,550] [INFO] Target genome list was writen to GCF_001312005.1_ASM131200v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:01:10,571] [INFO] Task started: fastANI
[2024-01-25 18:01:10,571] [INFO] Running command: fastANI --query /var/lib/cwl/stg3f19163a-bb77-4d17-9a58-761ed998c88c/GCF_001312005.1_ASM131200v1_genomic.fna.gz --refList GCF_001312005.1_ASM131200v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001312005.1_ASM131200v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:01:28,389] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:28,399] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:01:28,399] [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_001312005.1	s__Methylomonas koyamae	100.0	1450	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	96.46	95.49	0.87	0.86	5	conclusive
GCF_006483455.1	s__Methylomonas koyamae_B	86.8274	1049	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016865255.1	s__Methylomonas sp000702925	80.5913	683	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	97.47	95.82	0.92	0.86	5	-
GCF_903064685.1	s__Methylomonas sp903064685	80.4933	685	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001644025.1	s__Methylomonas koyamae_A	80.4833	619	1465	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	80.025	659	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	95.46	95.46	0.83	0.83	2	-
GCF_001644035.1	s__Methylomonas methanica_A	79.9528	655	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	95.96	95.96	0.85	0.85	2	-
GCA_001644045.1	s__Methylomonas methanica	79.873	680	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	99.99	99.99	1.00	0.99	3	-
GCF_015711015.1	s__Methylomonas sp015711015	79.5852	506	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903064715.1	s__Methylomonas sp903064715	79.4764	590	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008632455.1	s__Methylomonas rhizoryzae	79.1856	378	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018335995.1	s__Methylomonas sp018335995	79.0776	345	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000214665.1	s__Methylomonas methanica_B	78.2509	387	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903858105.1	s__Methylomonas sp903858105	78.2324	329	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000527095.1	s__Methylomicrobium lacus	77.0863	223	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903918375.1	s__Methylomonas sp903918375	76.8809	135	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	98.06	95.20	0.87	0.72	8	-
GCA_903931355.1	s__Methylomonas sp903931355	76.5045	90	1465	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:01:28,401] [INFO] GTDB search result was written to GCF_001312005.1_ASM131200v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:01:28,401] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:01:28,404] [INFO] DFAST_QC result json was written to GCF_001312005.1_ASM131200v1_genomic.fna/dqc_result.json
[2024-01-25 18:01:28,405] [INFO] DFAST_QC completed!
[2024-01-25 18:01:28,405] [INFO] Total running time: 0h1m23s