[2023-06-08 02:20:22,273] [INFO] DFAST_QC pipeline started.
[2023-06-08 02:20:22,280] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 02:20:22,281] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d4ca74d-379d-44df-8262-d82dbc13e574/dqc_reference
[2023-06-08 02:20:23,858] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 02:20:23,859] [INFO] Task started: Prodigal
[2023-06-08 02:20:23,859] [INFO] Running command: gunzip -c /var/lib/cwl/stg0aaecb1d-fa9f-4b92-856a-0b635786ce2a/GCA_945898035.1_MiH-14oct19-169_genomic.fna.gz | prodigal -d GCA_945898035.1_MiH-14oct19-169_genomic.fna/cds.fna -a GCA_945898035.1_MiH-14oct19-169_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 02:20:36,012] [INFO] Task succeeded: Prodigal
[2023-06-08 02:20:36,013] [INFO] Task started: HMMsearch
[2023-06-08 02:20:36,013] [INFO] Running command: hmmsearch --tblout GCA_945898035.1_MiH-14oct19-169_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d4ca74d-379d-44df-8262-d82dbc13e574/dqc_reference/reference_markers.hmm GCA_945898035.1_MiH-14oct19-169_genomic.fna/protein.faa > /dev/null
[2023-06-08 02:20:36,300] [INFO] Task succeeded: HMMsearch
[2023-06-08 02:20:36,302] [INFO] Found 6/6 markers.
[2023-06-08 02:20:36,342] [INFO] Query marker FASTA was written to GCA_945898035.1_MiH-14oct19-169_genomic.fna/markers.fasta
[2023-06-08 02:20:36,343] [INFO] Task started: Blastn
[2023-06-08 02:20:36,343] [INFO] Running command: blastn -query GCA_945898035.1_MiH-14oct19-169_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d4ca74d-379d-44df-8262-d82dbc13e574/dqc_reference/reference_markers.fasta -out GCA_945898035.1_MiH-14oct19-169_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:20:36,946] [INFO] Task succeeded: Blastn
[2023-06-08 02:20:36,950] [INFO] Selected 15 target genomes.
[2023-06-08 02:20:36,950] [INFO] Target genome list was writen to GCA_945898035.1_MiH-14oct19-169_genomic.fna/target_genomes.txt
[2023-06-08 02:20:36,953] [INFO] Task started: fastANI
[2023-06-08 02:20:36,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg0aaecb1d-fa9f-4b92-856a-0b635786ce2a/GCA_945898035.1_MiH-14oct19-169_genomic.fna.gz --refList GCA_945898035.1_MiH-14oct19-169_genomic.fna/target_genomes.txt --output GCA_945898035.1_MiH-14oct19-169_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 02:20:46,985] [INFO] Task succeeded: fastANI
[2023-06-08 02:20:46,985] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d4ca74d-379d-44df-8262-d82dbc13e574/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 02:20:46,986] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d4ca74d-379d-44df-8262-d82dbc13e574/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 02:20:46,988] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 02:20:46,988] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 02:20:46,989] [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
--------------------------------------------------------------------------------
[2023-06-08 02:20:46,991] [INFO] DFAST Taxonomy check result was written to GCA_945898035.1_MiH-14oct19-169_genomic.fna/tc_result.tsv
[2023-06-08 02:20:46,992] [INFO] ===== Taxonomy check completed =====
[2023-06-08 02:20:46,992] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 02:20:46,993] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d4ca74d-379d-44df-8262-d82dbc13e574/dqc_reference/checkm_data
[2023-06-08 02:20:46,998] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 02:20:47,041] [INFO] Task started: CheckM
[2023-06-08 02:20:47,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945898035.1_MiH-14oct19-169_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945898035.1_MiH-14oct19-169_genomic.fna/checkm_input GCA_945898035.1_MiH-14oct19-169_genomic.fna/checkm_result
[2023-06-08 02:21:26,951] [INFO] Task succeeded: CheckM
[2023-06-08 02:21:26,952] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 02:21:26,974] [INFO] ===== Completeness check finished =====
[2023-06-08 02:21:26,975] [INFO] ===== Start GTDB Search =====
[2023-06-08 02:21:26,975] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945898035.1_MiH-14oct19-169_genomic.fna/markers.fasta)
[2023-06-08 02:21:26,976] [INFO] Task started: Blastn
[2023-06-08 02:21:26,976] [INFO] Running command: blastn -query GCA_945898035.1_MiH-14oct19-169_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d4ca74d-379d-44df-8262-d82dbc13e574/dqc_reference/reference_markers_gtdb.fasta -out GCA_945898035.1_MiH-14oct19-169_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 02:21:27,747] [INFO] Task succeeded: Blastn
[2023-06-08 02:21:27,778] [INFO] Selected 16 target genomes.
[2023-06-08 02:21:27,778] [INFO] Target genome list was writen to GCA_945898035.1_MiH-14oct19-169_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 02:21:27,816] [INFO] Task started: fastANI
[2023-06-08 02:21:27,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg0aaecb1d-fa9f-4b92-856a-0b635786ce2a/GCA_945898035.1_MiH-14oct19-169_genomic.fna.gz --refList GCA_945898035.1_MiH-14oct19-169_genomic.fna/target_genomes_gtdb.txt --output GCA_945898035.1_MiH-14oct19-169_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 02:21:38,942] [INFO] Task succeeded: fastANI
[2023-06-08 02:21:38,958] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 02:21:38,958] [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_016234555.1	s__OLB14 sp016234555	78.0993	513	1350	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903837815.1	s__OLB14 sp903837815	78.0079	340	1350	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715195.1	s__OLB14 sp016715195	77.8191	355	1350	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	97.24	96.60	0.91	0.90	3	-
GCA_013140605.1	s__OLB14 sp013140605	77.6252	289	1350	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234535.1	s__OLB14 sp016234535	77.4899	286	1350	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016718275.1	s__OLB14 sp016718275	77.471	318	1350	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	98.35	98.30	0.92	0.91	3	-
GCA_903914955.1	s__OLB14 sp903914955	77.4543	271	1350	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	99.73	99.73	0.91	0.91	2	-
GCA_016219545.1	s__OLB14 sp016219545	77.4295	260	1350	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016234495.1	s__OLB14 sp016234495	77.4202	318	1350	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016866215.1	s__OLB14 sp016866215	77.3275	250	1350	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017985935.1	s__OLB14 sp017985935	77.1003	266	1350	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	99.53	99.53	0.94	0.94	2	-
GCA_016235445.1	s__OLB14 sp016235445	77.0164	265	1350	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789485.1	s__OLB14 sp016789485	76.8844	144	1350	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860745.1	s__OLB14 sp014860745	76.8629	231	1350	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003599285.1	s__OLB14 sp003599285	76.6466	136	1350	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789225.1	s__OLB14 sp016789225	76.5062	79	1350	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__OLB14	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 02:21:38,960] [INFO] GTDB search result was written to GCA_945898035.1_MiH-14oct19-169_genomic.fna/result_gtdb.tsv
[2023-06-08 02:21:38,960] [INFO] ===== GTDB Search completed =====
[2023-06-08 02:21:38,963] [INFO] DFAST_QC result json was written to GCA_945898035.1_MiH-14oct19-169_genomic.fna/dqc_result.json
[2023-06-08 02:21:38,964] [INFO] DFAST_QC completed!
[2023-06-08 02:21:38,964] [INFO] Total running time: 0h1m17s