[2024-01-24 14:06:44,428] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:44,429] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:44,430] [INFO] DQC Reference Directory: /var/lib/cwl/stg7bba804c-5d18-44ef-ace2-d6531a528708/dqc_reference
[2024-01-24 14:06:45,980] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:45,981] [INFO] Task started: Prodigal
[2024-01-24 14:06:45,982] [INFO] Running command: gunzip -c /var/lib/cwl/stg393a3ff4-f256-47cf-9a98-e1ab516dd3a1/GCF_025231485.1_ASM2523148v1_genomic.fna.gz | prodigal -d GCF_025231485.1_ASM2523148v1_genomic.fna/cds.fna -a GCF_025231485.1_ASM2523148v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:09,510] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:09,511] [INFO] Task started: HMMsearch
[2024-01-24 14:07:09,511] [INFO] Running command: hmmsearch --tblout GCF_025231485.1_ASM2523148v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7bba804c-5d18-44ef-ace2-d6531a528708/dqc_reference/reference_markers.hmm GCF_025231485.1_ASM2523148v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:09,782] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:09,783] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg393a3ff4-f256-47cf-9a98-e1ab516dd3a1/GCF_025231485.1_ASM2523148v1_genomic.fna.gz]
[2024-01-24 14:07:09,825] [INFO] Query marker FASTA was written to GCF_025231485.1_ASM2523148v1_genomic.fna/markers.fasta
[2024-01-24 14:07:09,825] [INFO] Task started: Blastn
[2024-01-24 14:07:09,825] [INFO] Running command: blastn -query GCF_025231485.1_ASM2523148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bba804c-5d18-44ef-ace2-d6531a528708/dqc_reference/reference_markers.fasta -out GCF_025231485.1_ASM2523148v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:10,354] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:10,357] [INFO] Selected 10 target genomes.
[2024-01-24 14:07:10,358] [INFO] Target genome list was writen to GCF_025231485.1_ASM2523148v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:10,364] [INFO] Task started: fastANI
[2024-01-24 14:07:10,364] [INFO] Running command: fastANI --query /var/lib/cwl/stg393a3ff4-f256-47cf-9a98-e1ab516dd3a1/GCF_025231485.1_ASM2523148v1_genomic.fna.gz --refList GCF_025231485.1_ASM2523148v1_genomic.fna/target_genomes.txt --output GCF_025231485.1_ASM2523148v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:19,467] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:19,467] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7bba804c-5d18-44ef-ace2-d6531a528708/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:19,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7bba804c-5d18-44ef-ace2-d6531a528708/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:19,477] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:19,477] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:19,478] [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
Salinirubellus salinus	strain=ZS-35-S2	GCA_025231485.1	1364945	1364945	type	True	100.0	1453	1458	95	conclusive
Haloglomus irregulare	strain=F16-60	GCA_007421925.1	2234134	2234134	type	True	79.0249	530	1458	95	below_threshold
Natronomonas salina	strain=YPL13	GCA_013391105.1	1710540	1710540	type	True	78.6909	519	1458	95	below_threshold
Haloarchaeobius salinus	strain=YC82	GCA_024464185.1	1198298	1198298	type	True	78.2787	476	1458	95	below_threshold
Natronomonas halophila	strain=C90	GCA_013391085.1	2747817	2747817	type	True	78.2129	386	1458	95	below_threshold
Halosegnis rubeus	strain=F17-44	GCA_009184545.1	2212850	2212850	type	True	78.1651	367	1458	95	below_threshold
Halosegnis longus	strain=F12-1	GCA_009663395.1	2216012	2216012	type	True	78.1307	381	1458	95	below_threshold
Halosimplex rubrum	strain=R27	GCA_013415885.1	869889	869889	type	True	77.7276	484	1458	95	below_threshold
Halosimplex carlsbadense	strain=2-9-1	GCA_000337455.1	171164	171164	type	True	77.6072	468	1458	95	below_threshold
Halogeometricum rufum	strain=CGMCC 1.7736	GCA_900112175.1	553469	553469	type	True	77.5483	519	1458	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:19,479] [INFO] DFAST Taxonomy check result was written to GCF_025231485.1_ASM2523148v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:19,480] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:19,480] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:19,480] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7bba804c-5d18-44ef-ace2-d6531a528708/dqc_reference/checkm_data
[2024-01-24 14:07:19,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:19,525] [INFO] Task started: CheckM
[2024-01-24 14:07:19,526] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025231485.1_ASM2523148v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025231485.1_ASM2523148v1_genomic.fna/checkm_input GCF_025231485.1_ASM2523148v1_genomic.fna/checkm_result
[2024-01-24 14:08:22,314] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:22,315] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:22,337] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:22,338] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:22,338] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025231485.1_ASM2523148v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:22,339] [INFO] Task started: Blastn
[2024-01-24 14:08:22,339] [INFO] Running command: blastn -query GCF_025231485.1_ASM2523148v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bba804c-5d18-44ef-ace2-d6531a528708/dqc_reference/reference_markers_gtdb.fasta -out GCF_025231485.1_ASM2523148v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:22,912] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:22,916] [INFO] Selected 13 target genomes.
[2024-01-24 14:08:22,916] [INFO] Target genome list was writen to GCF_025231485.1_ASM2523148v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:22,931] [INFO] Task started: fastANI
[2024-01-24 14:08:22,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg393a3ff4-f256-47cf-9a98-e1ab516dd3a1/GCF_025231485.1_ASM2523148v1_genomic.fna.gz --refList GCF_025231485.1_ASM2523148v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025231485.1_ASM2523148v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:33,402] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:33,414] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:08:33,414] [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_003022005.1	s__QS-5-70-15 sp003022005	79.6596	500	1458	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__QS-5-70-15	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007421925.1	s__Haloglomus irregulare	79.0107	533	1458	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Haloglomus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391105.1	s__Natronomonas salina	78.6962	519	1458	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009741925.1	s__Natronomonas sp009741925	78.2668	416	1458	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391635.1	s__Natronomonas gomsonensis	78.2573	428	1458	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391085.1	s__Natronomonas halophila	78.241	383	1458	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184545.1	s__CBA1134 sp009184545	78.1949	364	1458	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__CBA1134	95.0	99.60	99.56	0.94	0.94	3	-
GCA_007135435.1	s__Natronomonas sp007135435	77.9188	283	1458	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Natronomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003369835.1	s__Halorussus rarus	77.849	487	1458	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013415885.1	s__Halosimplex rubrum	77.718	487	1458	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337455.1	s__Halosimplex carlsbadense	77.6535	461	1458	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112175.1	s__Halogeometricum rufum	77.5602	515	1458	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogeometricum	95.0	98.26	98.26	0.87	0.87	2	-
GCA_003021655.1	s__QS-4-69-31 sp003021655	77.2555	350	1458	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__QS-4-69-31	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:33,416] [INFO] GTDB search result was written to GCF_025231485.1_ASM2523148v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:33,417] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:33,428] [INFO] DFAST_QC result json was written to GCF_025231485.1_ASM2523148v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:33,428] [INFO] DFAST_QC completed!
[2024-01-24 14:08:33,428] [INFO] Total running time: 0h1m49s