[2024-01-24 14:04:44,392] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:04:44,394] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:04:44,394] [INFO] DQC Reference Directory: /var/lib/cwl/stg1065c661-a4e8-4373-a56f-b71c2bde5285/dqc_reference
[2024-01-24 14:04:45,569] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:04:45,570] [INFO] Task started: Prodigal
[2024-01-24 14:04:45,570] [INFO] Running command: gunzip -c /var/lib/cwl/stg08b7c602-9838-4bda-b0c2-ffacf8789ec6/GCF_900128415.1_PRJEB15655_genomic.fna.gz | prodigal -d GCF_900128415.1_PRJEB15655_genomic.fna/cds.fna -a GCF_900128415.1_PRJEB15655_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:04:49,462] [INFO] Task succeeded: Prodigal
[2024-01-24 14:04:49,462] [INFO] Task started: HMMsearch
[2024-01-24 14:04:49,462] [INFO] Running command: hmmsearch --tblout GCF_900128415.1_PRJEB15655_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1065c661-a4e8-4373-a56f-b71c2bde5285/dqc_reference/reference_markers.hmm GCF_900128415.1_PRJEB15655_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:04:49,695] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:04:49,697] [INFO] Found 6/6 markers.
[2024-01-24 14:04:49,723] [INFO] Query marker FASTA was written to GCF_900128415.1_PRJEB15655_genomic.fna/markers.fasta
[2024-01-24 14:04:49,724] [INFO] Task started: Blastn
[2024-01-24 14:04:49,724] [INFO] Running command: blastn -query GCF_900128415.1_PRJEB15655_genomic.fna/markers.fasta -db /var/lib/cwl/stg1065c661-a4e8-4373-a56f-b71c2bde5285/dqc_reference/reference_markers.fasta -out GCF_900128415.1_PRJEB15655_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:50,313] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:50,317] [INFO] Selected 9 target genomes.
[2024-01-24 14:04:50,318] [INFO] Target genome list was writen to GCF_900128415.1_PRJEB15655_genomic.fna/target_genomes.txt
[2024-01-24 14:04:50,373] [INFO] Task started: fastANI
[2024-01-24 14:04:50,373] [INFO] Running command: fastANI --query /var/lib/cwl/stg08b7c602-9838-4bda-b0c2-ffacf8789ec6/GCF_900128415.1_PRJEB15655_genomic.fna.gz --refList GCF_900128415.1_PRJEB15655_genomic.fna/target_genomes.txt --output GCF_900128415.1_PRJEB15655_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:04:54,326] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:54,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1065c661-a4e8-4373-a56f-b71c2bde5285/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:04:54,327] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1065c661-a4e8-4373-a56f-b71c2bde5285/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:04:54,341] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:04:54,341] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:04:54,342] [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
Anaerococcus mediterraneensis	strain=Marseille-P2765	GCA_900128415.1	1870984	1870984	type	True	100.0	689	693	95	conclusive
Anaerococcus degeneri	strain=FDAARGOS_1538	GCA_020215685.1	361500	361500	type	True	82.9668	347	693	95	below_threshold
Anaerococcus murdochii	strain=FDAARGOS_1460	GCA_019957155.1	411577	411577	type	True	82.9601	349	693	95	below_threshold
Anaerococcus degeneri	strain=DSM 29674	GCA_017874475.1	361500	361500	type	True	82.8108	338	693	95	below_threshold
Anaerococcus lactolyticus	strain=ATCC 51172	GCA_000156575.1	33032	33032	type	True	82.424	314	693	95	below_threshold
Anaerococcus ihuae	strain=Marseille-Q5893	GCA_928368155.1	2899519	2899519	type	True	81.6447	123	693	95	below_threshold
Anaerococcus vaginimassiliensis	strain=Marseille-P4512	GCA_900626155.1	2042308	2042308	type	True	81.442	184	693	95	below_threshold
Anaerococcus marasmi	strain=Marseille-P3557	GCA_900290195.1	2057797	2057797	type	True	80.8721	162	693	95	below_threshold
Anaerococcus tetradius	strain=ATCC 35098	GCA_000159095.1	33036	33036	type	True	80.7502	168	693	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:04:54,343] [INFO] DFAST Taxonomy check result was written to GCF_900128415.1_PRJEB15655_genomic.fna/tc_result.tsv
[2024-01-24 14:04:54,346] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:04:54,346] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:04:54,347] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1065c661-a4e8-4373-a56f-b71c2bde5285/dqc_reference/checkm_data
[2024-01-24 14:04:54,348] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:04:54,378] [INFO] Task started: CheckM
[2024-01-24 14:04:54,378] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900128415.1_PRJEB15655_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900128415.1_PRJEB15655_genomic.fna/checkm_input GCF_900128415.1_PRJEB15655_genomic.fna/checkm_result
[2024-01-24 14:05:13,537] [INFO] Task succeeded: CheckM
[2024-01-24 14:05:13,538] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:05:13,556] [INFO] ===== Completeness check finished =====
[2024-01-24 14:05:13,557] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:05:13,557] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900128415.1_PRJEB15655_genomic.fna/markers.fasta)
[2024-01-24 14:05:13,558] [INFO] Task started: Blastn
[2024-01-24 14:05:13,558] [INFO] Running command: blastn -query GCF_900128415.1_PRJEB15655_genomic.fna/markers.fasta -db /var/lib/cwl/stg1065c661-a4e8-4373-a56f-b71c2bde5285/dqc_reference/reference_markers_gtdb.fasta -out GCF_900128415.1_PRJEB15655_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:14,367] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:14,371] [INFO] Selected 9 target genomes.
[2024-01-24 14:05:14,371] [INFO] Target genome list was writen to GCF_900128415.1_PRJEB15655_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:05:14,392] [INFO] Task started: fastANI
[2024-01-24 14:05:14,392] [INFO] Running command: fastANI --query /var/lib/cwl/stg08b7c602-9838-4bda-b0c2-ffacf8789ec6/GCF_900128415.1_PRJEB15655_genomic.fna.gz --refList GCF_900128415.1_PRJEB15655_genomic.fna/target_genomes_gtdb.txt --output GCF_900128415.1_PRJEB15655_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:05:18,395] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:18,407] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:05:18,407] [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_900128415.1	s__Anaerococcus mediterraneensis	100.0	688	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_017874475.1	s__Anaerococcus degeneri	82.8068	338	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000156575.1	s__Anaerococcus lactolyticus	82.4494	313	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	97.67	97.67	0.89	0.89	2	-
GCF_900626155.1	s__Anaerococcus vaginimassiliensis	81.4037	185	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	95.85	95.85	0.94	0.94	2	-
GCF_900258475.1	s__Anaerococcus sp900258475	81.1357	307	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	96.55	96.55	0.87	0.87	2	-
GCF_000312365.2	s__Anaerococcus provencensis	81.131	139	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900290195.1	s__Anaerococcus marasmi	80.7894	161	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000159095.1	s__Anaerococcus tetradius	80.7448	168	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	98.20	98.20	0.90	0.90	2	-
GCA_900551095.1	s__Anaerococcus sp900551095	79.9898	157	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:05:18,409] [INFO] GTDB search result was written to GCF_900128415.1_PRJEB15655_genomic.fna/result_gtdb.tsv
[2024-01-24 14:05:18,409] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:05:18,411] [INFO] DFAST_QC result json was written to GCF_900128415.1_PRJEB15655_genomic.fna/dqc_result.json
[2024-01-24 14:05:18,412] [INFO] DFAST_QC completed!
[2024-01-24 14:05:18,412] [INFO] Total running time: 0h0m34s